107 results on '"Scott A. Jackson"'
Search Results
2. Validation of resistance to root‐knot nematode incorporated in peanut from the wild relative Arachis stenosperma
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Soraya C. M. Leal-Bertioli, Peggy Ozias-Akins, Ye Chu, David J. Bertioli, Carolina Ballén-Taborda, Scott A. Jackson, and Patricia Timper
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Resistance (ecology) ,Arachis stenosperma ,Agronomy ,Root-knot nematode ,Biology ,biology.organism_classification ,Agronomy and Crop Science - Published
- 2021
3. Diet and bathymetric distribution of juvenile Lake Trout Salvelinus namaycush in Lake Huron
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Taaja R. Tucker, Dustin A. Bowser, Stephen C. Riley, Edward F. Roseman, Scott A. Jackson, and Steven A. Farha
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0106 biological sciences ,Ecology ,biology ,010604 marine biology & hydrobiology ,010501 environmental sciences ,Management, Monitoring, Policy and Law ,Aquatic Science ,biology.organism_classification ,01 natural sciences ,Fishery ,Trout ,Mysis ,Juvenile ,Bathymetry ,0105 earth and related environmental sciences ,Salvelinus - Abstract
Rehabilitation efforts for Lake Trout Salvelinus namaycush in Lake Huron have resulted in increased capture of young wild Lake Trout in annual bottom trawl surveys conducted by the U.S. Geological Survey. To better understand the ecology of juvenile (185 mm (∼age 2). The variety of taxa consumed by young Lake Trout increased with length. Further declines in Mysis populations due to increased predation pressure after the loss of Diporeia from the system may hinder the recovery of wild Lake Trout, and although they have been able to utilize invasive species as prey, impacts to Lake Trout growth remain unknown. Additional research on the habitat use and diets of wild juvenile Lake Trout may provide insight into the reasons behind the recent successful natural reproduction and recruitment of Lake Trout in Lake Huron.
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- 2020
4. Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature
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Elise Costa, Scott A. Jackson, and Leigh A. Frame
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0301 basic medicine ,Nutrition and Dietetics ,Medicine (miscellaneous) ,Microbial composition ,Context (language use) ,Nutrients ,Disease ,Biology ,Gut flora ,biology.organism_classification ,Bioinformatics ,Gut microbiome ,Diet ,Gastrointestinal Microbiome ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Intestinal transit ,Humans ,Nutritional Physiological Phenomena ,030211 gastroenterology & hepatology ,Dietary fiber ,Microbiome - Abstract
ContextThe ability to measure the gut microbiome led to a surge in understanding and knowledge of its role in health and disease. The diet is a source of fuel for and influencer of composition of the microbiome.ObjectiveTo assess the understanding of the interactions between nutrition and the gut microbiome in healthy adults.Data SourcesPubMed and Google Scholar searches were conducted in March and August 2018 and were limited to the following: English, 2010–2018, healthy adults, and reviews.Data ExtractionA total of 86 articles were independently screened for duplicates and relevance, based on preidentified inclusion criteria.Data AnalysisResearch has focused on dietary fiber – microbiota fuel. The benefits of fiber center on short-chain fatty acids, which are required by colonocytes, improve absorption, and reduce intestinal transit time. Contrastingly, protein promotes microbial protein metabolism and potentially harmful by-products that can stagnate in the gut. The microbiota utilize and produce micronutrients; the bidirectional relationship between micronutrition and the gut microbiome is emerging.ConclusionsNutrition has profound effects on microbial composition, in turn affecting wide-ranging metabolic, hormonal, and neurological processes. There is no consensus on what defines a “healthy” gut microbiome. Future research must consider individual responses to diet.
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- 2020
5. A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea)
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C. Corley Holbrook, David J. Bertioli, Scott A. Jackson, Soraya C. M. Leal-Bertioli, Ye Chu, Carolina Ballén-Taborda, Patricia Timper, and Peggy Ozias-Akins
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0106 biological sciences ,0301 basic medicine ,Arachis ,Quantitative Trait Loci ,Population ,lcsh:Medicine ,Biology ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,01 natural sciences ,Article ,Plant breeding ,03 medical and health sciences ,Plant hybridization ,Arachis batizocoi ,Animals ,Root-knot nematode ,Tylenchoidea ,Cultivar ,education ,lcsh:Science ,Disease Resistance ,Plant Proteins ,Genetics ,education.field_of_study ,Multidisciplinary ,fungi ,lcsh:R ,food and beverages ,biology.organism_classification ,Arachis hypogaea ,Tetraploidy ,030104 developmental biology ,Nematode ,lcsh:Q ,Ploidy ,010606 plant biology & botany - Abstract
Root-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma, [Arachis batizocoi x A. stenosperma]4×. This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma, is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.
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- 2019
6. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange
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Carolina Chavarro, Neil Halpin, Steven B. Cannon, H. T. Stalker, Dongying Gao, Shona Wood, Marcos Doniseti Michelotto, Walid Korani, Peggy Ozias-Akins, Soraya C. M. Leal-Bertioli, Andrew Farmer, João Francisco dos Santos, Scott A. Jackson, David J. Bertioli, Vania C. R. Azevedo, G. C. Wright, Daniel Fonceka, Carolina Ballén-Taborda, Brian E. Scheffler, Josh Clevenger, Brian Abernathy, Jane Grimwood, Ye Chu, Ignácio José de Godoy, Jacqueline D. Campbell, Ramey C Youngblood, Márcio C. Moretzsohn, and Justin N. Vaughn
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Germplasm ,Crops, Agricultural ,Genetic Markers ,disease resistance ,Asia ,Arachis ,DNA, Plant ,Oceania ,Biology ,Accession ,Species Specificity ,Convention on Biological Diversity ,Genetics ,Genetic diversity ,Multidisciplinary ,Food security ,business.industry ,Agricultural Sciences ,fungi ,food and beverages ,Chromosome Mapping ,Genetic Variation ,food security ,Biological Sciences ,biology.organism_classification ,Plant Breeding ,Agriculture ,wild species ,Africa ,Seeds ,Biological dispersal ,Hybridization, Genetic ,peanut ,sense organs ,business ,Arachis cardenasii ,Genome, Plant - Abstract
Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars with genetics from this wild accession provided improved food security and reduced use of fungicide sprays. However, this study also highlights the perilous consequences of changes in legal frameworks and attitudes concerning biodiversity. These changes have greatly reduced the botanical collections, seed exchanges, and international collaborations which are essential for the continued diversification of crop genetics and, consequently, the long-term resilience of crops against evolving pests and pathogens and changing climate., The narrow genetics of most crops is a fundamental vulnerability to food security. This makes wild crop relatives a strategic resource of genetic diversity that can be used for crop improvement and adaptation to new agricultural challenges. Here, we uncover the contribution of one wild species accession, Arachis cardenasii GKP 10017, to the peanut crop (Arachis hypogaea) that was initiated by complex hybridizations in the 1960s and propagated by international seed exchange. However, until this study, the global scale of the dispersal of genetic contributions from this wild accession had been obscured by the multiple germplasm transfers, breeding cycles, and unrecorded genetic mixing between lineages that had occurred over the years. By genetic analysis and pedigree research, we identified A. cardenasii–enhanced, disease-resistant cultivars in Africa, Asia, Oceania, and the Americas. These cultivars provide widespread improved food security and environmental and economic benefits. This study emphasizes the importance of wild species and collaborative networks of international expertise for crop improvement. However, it also highlights the consequences of the implementation of a patchwork of restrictive national laws and sea changes in attitudes regarding germplasm that followed in the wake of the Convention on Biological Diversity. Today, the botanical collections and multiple seed exchanges which enable benefits such as those revealed by this study are drastically reduced. The research reported here underscores the vital importance of ready access to germplasm in ensuring long-term world food security.
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- 2021
7. Short-chain diamines are the physiological substrates of PACE family efflux pumps
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Liping Li, Qi Liu, Jacob R. Edgerton, Leila Fahmy, Irshad Ahmad, Ian T. Paulsen, Karla A. Mettrick, Karl A. Hassan, Varsha Naidu, David Sharples, Peter J. F. Henderson, and Scott M. Jackson
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Acinetobacter baumannii ,Cadaverine transport ,Diamines ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Drug Resistance, Bacterial ,cardiovascular diseases ,030304 developmental biology ,0303 health sciences ,Cadaverine ,Multidisciplinary ,biology ,030306 microbiology ,Chemistry ,Chlorhexidine ,Membrane Transport Proteins ,Biological Sciences ,Membrane transport ,biology.organism_classification ,Anti-Bacterial Agents ,3. Good health ,Transport protein ,Putrescine ,Efflux ,Bacteria - Abstract
Acinetobacter baumannii has rapidly emerged as a major cause of gram-negative hospital infections worldwide. A. baumannii encodes for the transport protein AceI, which confers resistance to chlorhexidine, a widely used antiseptic. AceI is also the prototype for the recently discovered proteobacterial antimicrobial compound efflux (PACE) family of transport proteins that confer resistance to a range of antibiotics and antiseptics in many gram-negative bacteria, including pathogens. The gene encoding AceI is conserved in the core genome of A. baumannii, suggesting that it has an important primordial function. This is incongruous with the sole characterized substrate of AceI, chlorhexidine, an entirely synthetic biocide produced only during the last century. Here we investigated a potential primordial function of AceI and other members of the PACE family in the transport of naturally occurring polyamines. Polyamines are abundant in living cells, where they have physiologically important functions and play multifaceted roles in bacterial infection. Gene expression studies revealed that the aceI gene is induced in A. baumannii by the short-chain diamines cadaverine and putrescine. Membrane transport experiments conducted in whole cells of A. baumannii and Escherichia coli and also in proteoliposomes showed that AceI mediates the efflux of these short-chain diamines when energized by an electrochemical gradient. Assays conducted using 8 additional diverse PACE family proteins identified 3 that also catalyze cadaverine transport. Taken together, these results demonstrate that short-chain diamines are common substrates for the PACE family of transport proteins, adding to their broad significance as a novel family of efflux pumps.
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- 2019
8. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
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Gordon A. Awandare, Alistair Miles, Alister Craig, Nicholas J. White, Thanat Chookajorn, Colin J. Sutherland, Sarah Auburn, David J. Conway, Peter Siba, Xin-zhuan Su, Krzysztof Kluczynski, Kevin Marsh, Victoria Simpson, Mayfong Mayxay, Thuy-Nhien Nguyen, Thomas G. Egwang, Paul N. Newton, Lynette Isabella Ochola-Oyier, Lee Hart, Ambroise D. Ahouidi, Mallika Imwong, Alyssa E. Barry, Joseph M. Vinetz, Jacob Almagro-Garcia, Steffen Borrmann, Vito Baraka, MalariaGEN, Abraham Hodgson, Eleanor Drury, Aung Pyae Phyo, Marie A. Onyamboko, Jutta Marfurt, Jim Stalker, Christopher G Jacob, Ben Andagalu, Pascal Ringwald, Maciej F. Boni, Richard D. Pearson, Magnus Manske, Anita Ghansah, Rintis Noviyanti, Lastenia Ruiz, Umberto D'Alessandro, William L Hamilton, Sasithon Pukrittayakamee, Cinzia Malangone, Caterina A. Fanello, Philip Bejon, Julian C. Rayner, Lemu Golassa, Chris Drakeley, Nicholas P. J. Day, Thomas E. Wellems, Roberto Amato, Harald Noedl, Cristina V. Ariani, Alex Shayo, Arjen M. Dondorp, David L. Saunders, Rick M. Fairhurst, Catherine A. Hill, Christina Hubbart, Dominic P. Kwiatkowski, Olugbenga A. Mokuolu, Diego F. Echeverry, Alexis Nzila, Abdoulaye Djimde, Edwin Kamau, Chanaki Amaratunga, Myat Phone Kyaw, Chanthap Lon, Pharath Lim, Harold Ocholla, George B.J. Busby, Olivo Miotto, Kesinee Chotivanich, Christiane Dolecek, Ric N. Price, Kolapo Oyebola, Peter C. Bull, Dushyanth Jyothi, Brigitte Denis, Tobias O. Apinjoh, Lucas Amenga-Etego, Tim J. Anderson, Berhanu Erko, Mozam Ali, Claire Kamaliddin, Victor A. Mobegi, Hampate Ba, Christopher V. Plowe, Kimberly J. Johnson, Scott A. Jackson, Livingstone Tavul, Jacqui Montgomery, François Nosten, Thuy Nguyen, Abibatou Konaté, Mark M. Fukuda, Elizabeth A. Ashley, Dionicia Gamboa, William Yavo, G. L. Abby Harrison, Alfred Amambua-Ngwa, Mihir Kekre, Antoinette Tshefu, Tran Tinh Hien, Katherine Rowlands, Mahamadou Diakite, Ian J. Wright, Jason P. Wendler, Shannon Takala-Harrison, Htut Ye, Theerarat Kochakarn, Sónia Gonçalves, Vandana Thathy, Ben Jeffery, Kovana M. Loua, Ivo Mueller, Anna E. Jeffreys, Christa Henrichs, Teun Bousema, Antoine Claessens, Jean-Bosco Ouédraogo, Patrick E. Duffy, Voahangy Andrianaranjaka, Deus S. Ishengoma, Abraham Oduro, OraLee H. Branch, Abdul Faiz, Souleymane Dama, Federica Verra, Kirk A. Rockett, Gwladys I. Bertin, Oumou Maïga-Ascofaré, Milijaona Randrianarivelojosia, Irene Omedo, Norbert Peshu, LPHI - Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Intensive Care Medicine
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0301 basic medicine ,Population genetics ,Evolution ,purl.org/pe-repo/ocde/ford#1.06.03 [https] ,030231 tropical medicine ,Plasmodium falciparum ,Medicine (miscellaneous) ,Genomics ,Single-nucleotide polymorphism ,Drug resistance ,Biology ,General Biochemistry, Genetics and Molecular Biology ,purl.org/pe-repo/ocde/ford#3.00.00 [https] ,03 medical and health sciences ,0302 clinical medicine ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genotype ,parasitic diseases ,medicine ,qv_256 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Copy-number variation ,Indel ,Genetics ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Rapid diagnostic test failure ,medicine.disease ,biology.organism_classification ,Genomic epidemiology ,3. Good health ,wc_750 ,Malaria ,Data resource ,030104 developmental biology ,qx_510 ,qx_135 ,qu_470 - Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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- 2021
9. The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean
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Na Zhao, Xiaoyang Ding, Taotao Lian, Meng Wang, Yan Tong, Di Liang, Qi An, Siwen Sun, Scott A. Jackson, Bao Liu, and Chunming Xu
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0106 biological sciences ,0301 basic medicine ,duplicate gene ,lcsh:QH426-470 ,Glycine max ,Protein family ,01 natural sciences ,Genome ,03 medical and health sciences ,regulatory divergence ,Gene duplication ,Genetics ,soybean ,Gene ,Genetics (clinical) ,Original Research ,Hybrid ,Dominance (genetics) ,hybrid ,biology ,biology.organism_classification ,Glycine soja ,lcsh:Genetics ,030104 developmental biology ,Paleopolyploidy ,Molecular Medicine ,010606 plant biology & botany - Abstract
Regulatory changes include divergence in bothcis-elements andtrans-factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes inG. sojaandG. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance ofG. maxin their F1 hybrids. By classifying genes into different regulatory divergence types, we found thetrans-regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes ofcis-only between JY47 and GS, suggesting the substantial contribution ofcis-regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion ofcis-only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers ofcis-only andtrans-only regulated genes were similar for singletons, whereas there were more genes oftrans-only thancis-only in the rest duplication types, especially in WGD in which there were two times moretrans-only genes than that incis-only type. Tandem duplicates showed the highest proportion oftrans-only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned bycis- ortrans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.
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- 2020
10. Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses
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Hyein Jang, Hannah R. Chase, Jayanthi Gangiredla, Christopher J. Grim, Isha R. Patel, Mahendra H. Kothary, Scott A. Jackson, Mark K. Mammel, Laurenda Carter, Flavia Negrete, Samantha Finkelstein, Leah Weinstein, QiongQiong Yan, Carol Iversen, Franco Pagotto, Roger Stephan, Angelika Lehner, Athmanya K. Eshwar, Seamus Fanning, Jeffery Farber, Gopal R. Gopinath, Ben D. Tall, Monica Pava-Ripoll, University of Zurich, and Tall, Ben D
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Microbiology (medical) ,lcsh:QR1-502 ,Virulence ,610 Medicine & health ,Microbiology ,2726 Microbiology (medical) ,lcsh:Microbiology ,03 medical and health sciences ,Cronobacter turicensis ,Cronobacter dublinensis ,Cronobacter ,10082 Institute of Food Safety and Hygiene ,030304 developmental biology ,Original Research ,Whole genome sequencing ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,phylogenetic analysis ,2404 Microbiology ,Cronobacter malonaticus ,biology.organism_classification ,Cronobacter sakazakii ,flies as insects pests ,Cronobacter muytjensii ,whole-genome sequencing ,570 Life sciences ,microarray - Abstract
Cronobacter species are opportunistic pathogens capable of causing life-threatening infections in humans, with serious complications arising in neonates, infants, immuno-compromised individuals, and elderly adults. The genus is comprised of seven species: Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite a multiplicity of genomic data for the genus, little is known about likely transmission vectors. Using DNA microarray analysis, in parallel with whole genome sequencing, and targeted PCR analyses, the total gene content of two C. malonaticus, three C. turicensis, and 14 C. sakazaki isolated from various filth flies was assessed. Phylogenetic relatedness among these and other strains obtained during surveillance and outbreak investigations were comparatively assessed. Specifically, microarray analysis (MA) demonstrated its utility to cluster strains according to species-specific and sequence type (ST) phylogenetic relatedness, and that the fly strains clustered among strains obtained from clinical, food and environmental sources from United States, Europe, and Southeast Asia. This combinatorial approach was useful in data mining for virulence factor genes, and phage genes and gene clusters. In addition, results of plasmidotyping were in agreement with the species identity for each strain as determined by species-specific PCR assays, MA, and whole genome sequencing. Microarray and BLAST analyses of Cronobacter fly sequence datasets were corroborative and showed that the presence and absence of virulence factors followed species and ST evolutionary lines even though such genes were orthologous. Additionally, zebrafish infectivity studies showed that these pathotypes were as virulent to zebrafish embryos as other clinical strains. In summary, these findings support a striking phylogeny amongst fly, clinical, and surveillance strains isolated during 2010-2015, suggesting that flies are capable vectors for transmission of virulent Cronobacter spp.; they continue to circulate among United States and European populations, environments, and that this "pattern of circulation" has continued over decades.
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- 2020
11. The polyploid origins of crop genomes and their implications: A case study in legumes
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Scott A. Jackson and Brian D. Nadon
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education.field_of_study ,fungi ,Population ,food and beverages ,Biology ,biology.organism_classification ,Genome ,Crop ,Polyploid ,Evolutionary biology ,Gene duplication ,Faboideae ,Ploidy ,Domestication ,education - Abstract
Gene duplication and polyploidy are some of the most important, yet underappreciated, evolutionary forces that have shaped all flowering plants on earth, and the crop plants that enable human economic activity are prime exemplars of duplication in action. Polyploidy involves an immediate doubling, tripling, or more of a genome, often followed by drastic chromosomal reorganization or a reduction back to diploidy, and has occurred many times in the history of most characterized plant genomes. Understanding how duplication shapes plant genomes is critical for understanding how to feed a growing and hungry global human population. Of particular importance are legumes, one of the largest plant families on earth, often noted for their nitrogen fixation abilities and high nutritional value due to their protein content. Among these Papilionoid (Faboideae) legume crops are alfalfa, soybean, peanut, and common bean. All of these have experienced polyploidy events somewhere in their history, some ancient (60 My or more) and some very recent (e.g., ~ 10,000 years ago in peanut). The modes by which these polyploidies arose, whether from divergent genomes coming together (allopolyploidy), or identical or similar genomes duplicating (autopolyploidy), can affect their evolution, domestication, and improvement considerably, whether by generating new functional diversity or driving speciation. Appreciating the indelible mark polyploidy and duplication leave on these legume genomes will enable a better understanding of the molecular biology, breeding, and agronomy of these critical crops.
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- 2020
12. Parallel selection on a dormancy gene during domestication of crops from multiple families
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Yiqin Wang, Fanjiang Kong, Dali Zeng, Sijia Lu, Shu-Lin Liu, Jiuyou Tang, Chengcai Chu, Fan Xu, Rui Yang, Hongru Wang, Mingsheng Chen, Hao Lin, Baohui Liu, Wenzhen Li, Scott A. Jackson, Min Zhang, Yucheng Liu, Tao Lin, Zheng Wang, Chao Fang, Zhixi Tian, Baoge Zhu, and Min Wang
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Crops, Agricultural ,0301 basic medicine ,Arabidopsis ,Plant Development ,Sequence Homology ,Genetically modified crops ,Domestication ,03 medical and health sciences ,Solanum lycopersicum ,Genetics ,Plant breeding ,Selection, Genetic ,Gene ,biology ,fungi ,Seed dormancy ,food and beverages ,Agriculture ,Oryza ,Plant Dormancy ,Plants, Genetically Modified ,biology.organism_classification ,Genetically modified organism ,Plant Breeding ,030104 developmental biology ,Seeds ,Dormancy ,Soybeans - Abstract
Domesticated species often exhibit convergent phenotypic evolution, termed the domestication syndrome, of which loss of seed dormancy is a component. To date, dormancy genes that contribute to parallel domestication across different families have not been reported. Here, we cloned the classical stay-green G gene from soybean and found that it controls seed dormancy and showed evidence of selection during soybean domestication. Moreover, orthologs in rice and tomato also showed evidence of selection during domestication. Analysis of transgenic plants confirmed that orthologs of G had conserved functions in controlling seed dormancy in soybean, rice, and Arabidopsis. Functional investigation demonstrated that G affected seed dormancy through interactions with NCED3 and PSY and in turn modulated abscisic acid synthesis. Therefore, we identified a gene responsible for seed dormancy that has been subject to parallel selection in multiple crop families. This may help facilitate the domestication of new crops.
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- 2018
13. Hydrogenation of Naturally-Derived Nepetalactone as a Topical Insect Repellent
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Keith W. Hutchenson, Mark A. Scialdone, Leo Ernest Manzer, Bo Kou, Sourav K. Sengupta, David L. Hallahan, Yamaira Gonzalez, and Scott Christopher Jackson
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Active ingredient ,biology ,010405 organic chemistry ,Renewable Energy, Sustainability and the Environment ,Chemistry ,General Chemical Engineering ,030231 tropical medicine ,Nepeta cataria ,General Chemistry ,biology.organism_classification ,01 natural sciences ,0104 chemical sciences ,law.invention ,DEET ,03 medical and health sciences ,chemistry.chemical_compound ,Ingredient ,0302 clinical medicine ,Nepetalactone ,law ,Palladium on carbon ,Environmental Chemistry ,Organic chemistry ,Insect repellent ,Essential oil - Abstract
Dihydronepetalactone (DHN) is a safe and effective topical insect repellent,(5,6,8) comparable in efficacy to that of N,N-diethyl-m-toluamide (DEET). The latter is the most commonly used active ingredient, found in many commercial insect repellents for a broad range of biting insects. DHN can be produced by hydrogenating nepetalactone (NL), which is the primary ingredient of the essential oil obtained from the renewably sourced catmint plant, Nepeta cataria. Optimizing the hydrogenation reaction to produce DHN from catmint oil is a key economic driver for the process. Prior to the study described here, Six Sigma methodologies were used to select palladium on carbon (5% Pd/C) as the catalyst of choice. The hydrogenation step was studied as a function of critical process variables and the composition of the oil. As described in this article, a robust, two-step hydrogenation process was developed to maximize the yield of the desired DHNs from treated catmint oil. It was observed that the composition of the c...
- Published
- 2018
14. Genetic and epigenetic divergence of duplicate genes in two legume species
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Scott A. Jackson, Chunming Xu, Brian D. Nadon, and Kyung Do Kim
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0106 biological sciences ,0301 basic medicine ,Physiology ,Plant Science ,Biology ,Genes, Plant ,01 natural sciences ,Epigenesis, Genetic ,Evolution, Molecular ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genes, Duplicate ,Gene Duplication ,Gene expression ,Gene duplication ,Epigenetics ,Gene ,Phaseolus ,Genetics ,Methylation ,DNA Methylation ,biology.organism_classification ,Genetics, Population ,030104 developmental biology ,DNA methylation ,Neofunctionalization ,Soybeans ,Genome, Plant ,010606 plant biology & botany - Abstract
Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a polyploidy event ~59 MYA, followed by a Glycine-specific whole genome duplication (WGD) ~8-13 MYA. Duplicated genes were classified into five categories: singletons, dispersed, proximal, tandem, or WGD/segmental and found strong correlations between gene category and functional annotation. Photosynthesis and transcriptional regulation-related Gene Ontology terms were significantly over-represented in singletons and WGD genes, respectively, aligning with the gene balance hypothesis. We found that the divergence of gene expression and DNA methylation between WGD-derived paralogs increased with age and that WGD genes, initially retained via dosage constraints, subsequently underwent expression divergence, associated with other factors such as DNA methylation. Genes derived from different modes of duplication differed in breadth, level, and specificity of expression in both species. Orthologous genes and ungrouped genes (genes not in an ortholog group) differed in expression patterns. The protein divergence rates of WGD paralog pairs containing an ungrouped gene were higher than those for which both copies had orthologs. We propose that many ungrouped genes are derived from divergent and redundant gene copies, concordant with the neofunctionalization hypothesis. Tandemly duplicated genes were distinct from WGD-derived genes, indicating that mode of duplication contributes to the evolutionary fate of duplicated genes.
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- 2018
15. An assessment of iron and calcium amendments for managing phosphorus release from impacted Everglades soils
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Forrest E. Dierberg, Delia Ivanoff, Scott D. Jackson, Stacey C. Galloway, Michelle D. Kharbanda, Patrick D. Owens, and Thomas A. DeBusk
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0106 biological sciences ,chemistry.chemical_classification ,Typha domingensis ,biology ,010604 marine biology & hydrobiology ,Soil organic matter ,Amendment ,Soil classification ,Management, Monitoring, Policy and Law ,Aquatic Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,chemistry.chemical_compound ,Agronomy ,chemistry ,Soil pH ,Glyphosate ,Soil water ,Environmental science ,Organic matter ,Ecology, Evolution, Behavior and Systematics - Abstract
The recent implementation of agricultural best management practices (BMPs) and treatment wetlands called stormwater treatment areas (STAs) have reduced phosphorus (P) concentrations and loadings to the Everglades Protection Area (EPA) in Florida (USA). There is a concern that despite reductions in external P loadings, internal loading from the legacy P enrichment of the EPA wetland soils will continue to elevate water column P concentrations, and may impede restoration outcomes. In an effort to explore ways to reduce soil P efflux, we retrieved intact, vegetated (cattail, Typha domingensis) soil monoliths from two P-enriched areas of the EPA and deployed them at a location where they received pre-treated (low P) surface water as ex situ flow-through mesocosms for 21 months with a mid-study 7-week dry down to mimic natural hydroperiod conditions. Two treatments were tested for soils from both sites, using triplicate mesocosms for each treatment. After applying a herbicide (glyphosate) to eliminate the cattail vegetation, iron (Fe as liquid FeCl3) amendments provided no P retention benefits in the organic soils from the two sites, and did not yield significantly (P > 0.05; n = 43) lower flux rates (6.1 and 3.5 mg Pm−2 d−1) than the herbicide/no soil amendment control (3.9 and 2.1 mg Pm−2 d−1), as was expected. A combination of low oxidation–reduction potential, heightened organic matter P mineralization, high pH, and sulfide production acted interactively to enhance Fe and P mobilization in the Fe-amended mesocosms. The herbicide/limerock (CaCO3)-amended soils exhibited significantly lower (P ≤ 0.05; n = 43) P flux (1.3 and 1.1 mg Pm−2 d−1) than the herbicide/no soil amendment control soils, but it remains unknown whether the observed reduction in P efflux (ranging from 48 to 67%) would justify the expense and potential environmental impacts of applying a surficial limerock amendment to large regions of the P-enriched wetlands.
- Published
- 2017
16. Current Explorations of Nutrition and the Gut Microbiome: A Systematic Review (P20-032-19)
- Author
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Elise Costa, Scott A. Jackson, and Leigh A. Frame
- Subjects
Nutrition and Dietetics ,biology ,digestive, oral, and skin physiology ,Medicine (miscellaneous) ,High-protein diet ,Disease ,Gut flora ,Micronutrient ,medicine.disease_cause ,Bioinformatics ,biology.organism_classification ,digestive system ,Gut microbiome ,Nutritional Microbiology ,medicine ,Dietary fiber ,Disease prevention ,Microbiome ,Food Science - Abstract
OBJECTIVES: The ability to measure and describe the microbiome has led to a surge in information about the gut microbiome and its role in health and disease. The relationship between nutrition and the gut microbiome is central, as the diet is a source of microbiota, a source of fuel for the microbiota, and an indicator of the composition of the gut microbiome. We aim to assess the current understanding of the interactions between nutrition and the gut microbiome in healthy adults. A solid understanding of the interactions between nutrition and a healthy gut microbiome will form the foundation for understanding the role in disease prevention and treatment. METHODS: PubMed and Google Scholar searches for review articles relating to nutrition and the gut microbiome in healthy adults led to the inclusion of 38 articles in this systematic review. RESULTS: Much of the research has focused on carbohydrates in the form of dietary fiber, which are fuel for the gut microbiota. The beneficial effects of fiber have centered on Short Chain Fatty Acids (SCFAs) that are required by colonocytes (barrier function), improve absorption (minerals, water), and reduce intestinal transit time (colon cancer). Contrastingly, a low fiber, high protein diet promotes microbial protein metabolism, leading to potentially dangerous by-products that can stagnate in the gut. The bidirectional relationship between micronutrition and the gut microbiome is emerging. The microbiota utilize and produce micronutrients, leading to confounding relationships between nutritional status and biologic micronutrient concentrations, chiefly the B and K vitamins. While promising, the study of non-nutritive food components (polyphenols) and the gut microbiome is in its infancy. The role of other food components (food additives, contaminants) warrant exploration and are a significant research gap to-date. CONCLUSIONS: Diet and nutrition have profound effects on the gut microbiome composition. This, in turn, affects a wide array of metabolic, hormonal, and neurological processes that influence our health and disease. Currently, there is no consensus in the scientific community on what defines a “healthy” gut microbiome. Future research must consider individual responses to diet and the role of diet in the response of the gut microbiome to interventions. FUNDING SOURCES: N/A. SUPPORTING TABLES, IMAGES AND/OR GRAPHS
- Published
- 2019
17. Construction and comparison of three reference-quality genome assemblies for soybean
- Author
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Babu Valliyodan, Jacqueline Batley, Philipp E. Bayer, Robert M. Stupar, David Edwards, David Goodstein, Qijian Song, Yuxuan Yuan, Gunvant Patil, Henry T. Nguyen, Ting-Fung Chan, Christopher Daum, Jeremy Schmutz, Anne V. Brown, Shengqiang Shu, Claire Yik Lok Chung, Scott A. Jackson, Kobi Baruch, Gary Stacey, Jerry Jenkins, Wei Huang, Kerrie Barry, Longhui Ren, Hon-Ming Lam, Steven B. Cannon, Rajeev K. Varshney, Christopher Plott, Alex Hastie, Haifei Hu, and Jane Grimwood
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Glycine max ,Plant Biology ,Plant Science ,comparative genomics ,01 natural sciences ,Genome ,Repetitive Sequences ,Phylogeny ,Disease Resistance ,2. Zero hunger ,Fabaceae ,Single Nucleotide ,Telomere ,Multigene Family ,Genome, Plant ,Genotype ,Population ,Plant Biology & Botany ,Centromere ,Quantitative Trait Loci ,Introgression ,Genomics ,Locus (genetics) ,Biology ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,domestication ,Hardness ,Genetics ,Polymorphism ,soybean ,Domestication ,Alleles ,Repetitive Sequences, Nucleic Acid ,Nucleic Acid ,Sequence Inversion ,Haplotype ,Genetic Variation ,Cell Biology ,Plant ,15. Life on land ,biology.organism_classification ,Glycine soja ,030104 developmental biology ,Genetics, Population ,Haplotypes ,Evolutionary biology ,Seed Bank ,genome assembly ,Biochemistry and Cell Biology ,010606 plant biology & botany - Abstract
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G.max. The G.max assemblies provided are for widely used US cultivars: the northern line Williams82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G.soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7snpsperkb between these lines and G.soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G.soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G.soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
- Published
- 2018
18. Draft Genome Sequences of 72 Isolates from All Four Species of Shigella
- Author
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Christopher A. Elkins, David W. Lacher, Jayanthi Gangiredla, Scott A. Jackson, Mark K. Mammel, Amit Mukherjee, Carmen Tartera, and Isha R. Patel
- Subjects
Shigellosis ,Gram-negative bacteria ,Shigella dysenteriae ,biology ,Dysentery ,Pathogenic bacteria ,medicine.disease ,biology.organism_classification ,medicine.disease_cause ,Genome ,Microbiology ,Immunology and Microbiology (miscellaneous) ,Genetics ,medicine ,Shigella ,Molecular Biology ,Bacteria - Abstract
Shigella is a genus of Gram-negative enteric pathogenic bacteria which has four species, Shigella dysenteriae , S. flexneri , S. boydii , and S. sonnei . Shigella species are clinically important bacteria because they cause shigellosis or dysentery.
- Published
- 2018
19. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
- Author
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Ann Danowitz, Shu-Min Kao, Manyuan Long, Thomas Wicker, Andrea R. Gschwend, Chengjun Zhang, Jayson Talag, Dave Flowers, Railson Schreinert dos Santos, Derrick J. Zwickl, Bin Han, Jetty S.S. Ammiraju, Seunghee Lee, Claude Becker, Muhua Wang, Scott A. Jackson, Qi Feng, Ramil Mauleon, Kshirod K. Jena, Luis F. Rivera, Moaine El Baidouri, Jeremy Schmutz, Eric Lasserre, Kevin G. Nyberg, Jhih wun Zeng, Robert J Henry, Jose Luis Goicoechea, Carlos A. Machado, Daniel da Rosa Farias, Michael J. Sanderson, Kapeel Chougule, Jianwei Zhang, Nori Kurata, Yi Liao, Julie Jacquemin, Yeisoo Yu, Christos Noutsos, Chuanzhu Fan, Joshua C. Stein, Richard Cooke, Rod A. Wing, Marie-Christine Carpentier, Aiko Iwata, Dongying Gao, Carlos E.M. Londono, Nickolai Alexandrov, Olivier Panaud, Kenneth L. McNally, Xiang Song, Li Zhang, Cheng chieh Wu, Antonio Costa de Oliveira, Dario Copetti, Andrea Zuccolo, Fu Jin Wei, Mingsheng Chen, Sharon Wei, Dave Kudrna, Yue-Ie C. Hsing, Doreen Ware, Jun Wang, Detlef Weigel, Paul L. Sanchez, Luciano Carlos da Maia, and Qiang Zhao
- Subjects
0301 basic medicine ,Plant genetics ,Genomics ,Biology ,Oryza ,biology.organism_classification ,Genome ,03 medical and health sciences ,030104 developmental biology ,Genus ,Evolutionary biology ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,Genetics ,Domestication - Abstract
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.
- Published
- 2018
20. Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris)
- Author
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Dongyan Zhao, Scott A. Jackson, Brian Abernathy, Dongying Gao, Ning Jiang, Aiko Iwata-Otsubo, and Alfredo Herrera-Estrella
- Subjects
0106 biological sciences ,0301 basic medicine ,Transposable element ,Genome evolution ,Genetic Speciation ,Investigations ,genome evolution ,QH426-470 ,01 natural sciences ,Genome ,Transposition (music) ,03 medical and health sciences ,Sequence Homology, Nucleic Acid ,CACTA ,Genetics ,DNA transposon ,Molecular Biology ,Gene ,In Situ Hybridization, Fluorescence ,Phylogeny ,Genetics (clinical) ,Plant Proteins ,common bean ,Phaseolus ,Base Sequence ,biology ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,030104 developmental biology ,DNA Transposable Elements ,Gene pool ,Sequence Alignment ,Genome, Plant ,010606 plant biology & botany - Abstract
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
- Published
- 2016
21. Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives
- Author
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Scott A. Jackson, C. Eduardo Vallejos, Brian Abernathy, Aiko Iwata-Otsubo, Seth D. Findley, and Brittany Radke
- Subjects
0301 basic medicine ,medicine.medical_specialty ,Centromere ,Karyotype ,chromosome evolution ,Investigations ,QH426-470 ,Genes, Plant ,DNA, Ribosomal ,Evolution, Molecular ,03 medical and health sciences ,Species Specificity ,medicine ,Genetics ,Molecular Biology ,fluorescence in situ hybridization ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Phylogeny ,Repetitive Sequences, Nucleic Acid ,Phaseolus ,common bean ,biology ,medicine.diagnostic_test ,Base Sequence ,Cytogenetics ,Chromosome ,Genetic Variation ,food and beverages ,karyotyping ,biology.organism_classification ,Subtelomere ,satellite repeats ,030104 developmental biology ,Gene pool ,Fluorescence in situ hybridization - Abstract
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.
- Published
- 2016
22. Analysis of simple sequence repeats in rice bean ( Vigna umbellata ) using an SSR-enriched library
- Author
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Lixia Wang, Xuzhen Cheng, Scott A. Jackson, Suk-Ha Lee, Kyung Do Kim, Dongying Gao, Honglin Chen, and Suhua Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,food.ingredient ,Vigna umbellata ,Plant Science ,Quantitative trait locus ,01 natural sciences ,Distribution and frequency ,lcsh:Agriculture ,Vigna ,03 medical and health sciences ,food ,Botany ,Genomic library ,lcsh:Agriculture (General) ,Gene ,Molecular breeding ,biology ,lcsh:S ,food and beverages ,biology.organism_classification ,SSR ,lcsh:S1-972 ,030104 developmental biology ,Mapping ,Primer design ,Microsatellite ,Primer (molecular biology) ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice bean and other Vigna species.
- Published
- 2016
23. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
- Author
-
Seunghee Lee, Jetty S.S. Ammiraju, Railson Schreinert dos Santos, Ann Danowitz, Shu-Min Kao, Li Zhang, Chengjun Zhang, Cheng chieh Wu, Dongying Gao, Carlos E.M. Londono, Scott A. Jackson, Yi Liao, Mingsheng Chen, Chuanzhu Fan, Andrea Zuccolo, Muhua Wang, Christos Noutsos, Rod A. Wing, Manyuan Long, Robert J Henry, Marie-Christine Carpentier, Kshirod K. Jena, Aiko Iwata, Yue-Ie C. Hsing, Jose Luis Goicoechea, Bin Han, Richard Cooke, Joshua C. Stein, Luis F. Rivera, Thomas Wicker, Dario Copetti, Fu Jin Wei, Claude Becker, Paul L. Sanchez, Qi Feng, Andrea R. Gschwend, Ramil Mauleon, Carlos A. Machado, Derrick J. Zwickl, Daniel da Rosa Farias, Jayson Talag, Dave Flowers, Eric Lasserre, Nickolai Alexandrov, Yeisoo Yu, Moaine El Baidouri, Luciano Carlos da Maia, Jeremy Schmutz, Dave Kudrna, Olivier Panaud, Kenneth L. McNally, Xiang Song, Kevin G. Nyberg, Nori Kurata, Qiang Zhao, Kapeel Chougule, Jhih wun Zeng, Antonio Costa de Oliveira, Jianwei Zhang, Doreen Ware, Jun Wang, Detlef Weigel, Sharon Wei, Julie Jacquemin, Michael J. Sanderson, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Dipartimento Sci Agr & Ambientali, Università degli Studi di Udine - University of Udine [Italie], Wuhan University [China], University of Georgia [USA], Chinese Academy of Agricultural Mechanization Sciences (CCCME), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Tsukuba University of Technology, Graduate School of Comprehensive Human Sciences, Université de Tsukuba = University of Tsukuba, Sismologie (IPGS) (IPGS-Sismologie), Institut de physique du globe de Strasbourg (IPGS), Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Institute of Plant Biology, University of Zurich, Plant Genomics and Breeding Center, Department of Biology, and Cold Spring Harbor Laboratory
- Subjects
0301 basic medicine ,Crops, Agricultural ,Evolution ,Genetic Speciation ,[SDV]Life Sciences [q-bio] ,Plant genetics ,Introgression ,Genomics ,Crops ,Oryza ,Genome ,Medical and Health Sciences ,Evolution, Molecular ,Domestication ,03 medical and health sciences ,Molecular evolution ,Phylogenetics ,Genetics ,ComputingMilieux_MISCELLANEOUS ,Phylogeny ,Conserved Sequence ,2. Zero hunger ,Agricultural ,biology ,food and beverages ,Molecular ,Genetic Variation ,Plant ,15. Life on land ,Biological Sciences ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Genome, Plant ,Developmental Biology - Abstract
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.
- Published
- 2018
24. Identification of QTLs for Rust Resistance in the Peanut Wild Species Arachis magna and the Development of KASP Markers for Marker-Assisted Selection
- Author
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Soraya C. M. Leal-Bertioli, Patricia M. Guimarães, Márcio C. Moretzsohn, Scott A. Jackson, David J. Bertioli, Kenta Shirasawa, Carolina Ballén-Taborda, Ediene G. Gouvea, and Uiara Cavalcante
- Subjects
Genetic Markers ,Germplasm ,Arachis ,DNA, Plant ,Genetic Linkage ,Quantitative Trait Loci ,Population ,Introgression ,molecular breeding ,Investigations ,Breeding ,Plant disease resistance ,Polymorphism, Single Nucleotide ,marker-assisted selection ,Arachis ipaensis ,Species Specificity ,Botany ,Genetics ,education ,Molecular Biology ,Alleles ,Genetics (clinical) ,Disease Resistance ,education.field_of_study ,Base Sequence ,biology ,Chromosome Mapping ,food and beverages ,rust ,Sequence Analysis, DNA ,Marker-assisted selection ,biology.organism_classification ,Tetraploidy ,Phenotype ,peanut ,Gene pool ,Genome, Plant ,Microsatellite Repeats - Abstract
Rust is a major pathogen of the peanut crop. Development and adoption of rust-resistant cultivars is the most cost efficient and effective way to control the spread of the disease and reduce yield losses. Some cultivated peanut germplasm accessions have a degree of resistance, but the secondary gene pool is a source of much stronger resistance alleles. Wild species, however, have undesirable agronomic traits that are a disincentive to their use in breeding. The identification of genomic regions that harbor disease resistance in wild species is the first step in the implementation of marker-assisted selection that can speed the introgression of wild disease resistances and the elimination of linkage drag. In this work, we identify genome regions that control different components of rust resistance in a recombinant inbred line population developed from a cross between two Arachis species, the susceptible most probable B genome ancestor of cultivated peanut, Arachis ipaënsis, and an accession of its closest relative, Arachis magna, which is resistant to rust. Quantitative trait loci for several components of resistance were placed in the same position on linkage group B08. Single-nucleotide polymorphism Kompetitive allele-specific polymerase chain reaction markers for rust resistance region were designed and validated for marker function in both diploid and tetraploid contexts.
- Published
- 2015
25. Sulfide concentration effects on Typha domingensis Pers. (cattail) and Cladium jamaicense Crantz (sawgrass) growth in Everglades marshes
- Author
-
Binhe Gu, Thomas A. DeBusk, Dawn Sierer-Finn, Stacey C. Galloway, Forrest E. Dierberg, Scott D. Jackson, William F. DeBusk, and Janelle A. Potts
- Subjects
chemistry.chemical_classification ,Typha ,geography ,Marsh ,geography.geographical_feature_category ,Typha domingensis ,biology ,Sulfide ,Phosphorus ,chemistry.chemical_element ,Plant Science ,Aquatic Science ,biology.organism_classification ,Nutrient ,chemistry ,Botany ,Environmental science ,Surface water ,Cladium - Abstract
Displacement of large areas of native Cladium jamaicense Crantz (sawgrass) by Typha domingensis Pers. (cattail) in the Everglades has occurred during the past several decades, and is widely attributed to phosphorus (P) enrichment. In addition, sulfide toxicity to marsh vegetation, particularly Cladium , has been cited as a possible consequence of increased loading of sulfate to the Everglades (USA) from anthropogenic sources, and a potential contributor to the shift from Cladium to Typha . We initiated a plant growth study at three “low P” sites in the Everglades with differing surface water sulfate (1–48 mg L −1 ) and porewater sulfide (0.09–8.0 mg L −1 ) concentrations. Leaf elongation (LE) rates of Cladium and Typha were monitored, along with surface and porewater concentrations of iron, nutrients, and inorganic sulfur species. During the course of the study, we observed no reduction in Cladium or Typha LE rates at the two sulfate-impacted locations, relative to LE at a sulfate-unimpacted site. Moreover, across all study sites, we observed a positive, instead of a negative, relationship between Cladium LE rates and porewater sulfide concentrations. This suggests overriding effects of other factors such as P availability and supply on plant growth in these low-P environments, which was supported by a positive relationship between dissolved porewater P concentrations and Cladium LE rates, and by the Typha to Cladium LE ratios.
- Published
- 2015
26. Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis
- Author
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Brian Abernathy, David J. Bertioli, Kenta Shirasawa, Scott A. Jackson, Peggy Ozias-Akins, Carolina Chavarro, Soraya C. M. Leal-Bertioli, Márcio C. Moretzsohn, and Josh Clevenger
- Subjects
Arachis ,Genetic Linkage ,Quantitative Trait Loci ,Plant genetics ,groundnut ,tetrasomic genetics ,Investigations ,Quantitative trait locus ,Genome ,Chromosomes, Plant ,segmental genetics ,Genome Integrity and Transmission ,Inbred strain ,Genetic linkage ,Genetic model ,Genetics ,Recombination, Genetic ,Models, Genetic ,biology ,food and beverages ,biology.organism_classification ,Tetrasomy ,peanut ,induced allotetraploid ,Recombination - Abstract
Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut’s most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a “segmental allotetraploid” with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
- Published
- 2015
27. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology
- Author
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Laurenda Carter, Ben D. Tall, Isha R. Patel, Roger Stephan, Franco Pagotto, Mark K. Mammel, Gopal R. Gopinath, Jeffery Farber, Christopher J. Grim, Scott A. Jackson, Séamus Fanning, Angelika Lehner, Mahendra H. Kothary, Qiong Q. Yan, Jayanthi Gangiredla, Venugopal Sathyamoorthy, Carol Iversen, and University of Zurich
- Subjects
0301 basic medicine ,1303 Biochemistry ,030106 microbiology ,Biomedical Engineering ,2204 Biomedical Engineering ,Bioengineering ,Genomics ,610 Medicine & health ,Review ,Biochemistry ,Microbiology ,lcsh:Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Cronobacter dublinensis ,030225 pediatrics ,lcsh:QD415-436 ,Cronobacter ,Genotyping ,10082 Institute of Food Safety and Hygiene ,Genetics ,biology ,1502 Bioengineering ,Enterobacter ,data mining ,biology.organism_classification ,Cronobacter sakazakii ,genomic DNA ,1305 Biotechnology ,570 Life sciences ,DNA microarray ,microarray ,Biotechnology - Abstract
Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1) the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3) lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of this review is to describe microarrays as a robust tool for genomics research of this assorted and important genus, a criterion toward the development of future preventative measures to eliminate this foodborne pathogen from the global food supply.
- Published
- 2017
28. The Pigeonpea Genome
- Author
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Scott A. Jackson, Rachit K. Saxena, and Rajeev K. Varshney
- Subjects
Crop ,Cajanus ,biology ,Agroforestry ,Agriculture ,business.industry ,Genomics ,Plant breeding ,business ,biology.organism_classification ,Domestication ,Genome ,Arid - Abstract
Pigeonpea (Cajanus cajan) is a crop of small land holding farmers in arid and semi-arid regions of the world. It has a number of usages starting from protein rich food to vegetarian families; fuel wood; nitrogen supplier to soil; recycling minerals in soil to animal feed etc. Pigeonpea has been considered to be originated and domesticated in central India from where it travelled to different parts of the world such as Africa and Latin America. In ongoing scenario of climate change, biotic and especially abiotic stresses will make the conditions more challenging for entire agriculture. This volume focusing on the pigeonpea genome will collate the information on the genome sequencing and its utilization in genomics activities, with a focus on the current findings, advanced tools and strategies deployed in pigeonpea genome sequencing and analysis, and how this information is leading to direct outcomes for plant breeders and subsequently to farmers.
- Published
- 2017
29. Sequencing Ancestor Diploid Genomes for Enhanced Genome Understanding and Peanut Improvement
- Author
-
Rajeev K. Varshney, Scott A. Jackson, Xuanqiang Liang, Spurthi N. Nayak, and Manish K. Pandey
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Arachis ,food and beverages ,Sequence assembly ,Genomics ,Biology ,biology.organism_classification ,01 natural sciences ,Genome ,DNA sequencing ,03 medical and health sciences ,030104 developmental biology ,Ploidy ,Gene ,010606 plant biology & botany ,Genomic organization - Abstract
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. To understand the genome of the cultivated peanut, it is prerequisite to know the genome organization of its diploid progenitors, A-genome—Arachis duranensis and B-genome—A. ipaensis. Two genome sequencing projects conducted sequencing and analysis of the genomes of diploid ancestors: (1) International Peanut Genome Initiative (IPGI) reported the sequencing of both A- and B-genomes; while (2) Diploid Progenitor Peanut Arachis Genome Sequencing Consortium (DPPAGSC) reported the sequencing of A-genome. IPGI study showed that these genomes are similar to cultivated peanut’s A- and B-subgenomes and used them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut’s subgenomes thus providing evidence about direct descendant of the B subgenome in cultivated peanut. The DPPAGSC study, on the other hand, provided new insights into geocarpy, oil biosynthesis, and allergens in addition to providing information about evolution and polyploidization. These genome sequencing efforts have improved the understanding about the complex peanut genome and genome architecture which will play a very important role in peanut applied genomics and breeding.
- Published
- 2017
30. Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut
- Author
-
Soraya C. M. Leal-Bertioli, Annapurna Chitikineni, Manda Sriswathi, Manish K. Pandey, Scott A. Jackson, Peggy Ozias-Akins, David J. Bertioli, Josh Clevenger, Manish K. Vishwakarma, Carolina Chavarro, Baozhu Guo, Sandip M. Kale, Xiaoping Chen, Xuanqiang Liang, Spurthi N. Nayak, Hari D. Upadhyaya, Rajeev K. Varshney, and Gaurav Agarwal
- Subjects
0106 biological sciences ,0301 basic medicine ,Arachis ,Genotype ,Genotyping Techniques ,Context (language use) ,Biology ,Breeding ,01 natural sciences ,Polymorphism, Single Nucleotide ,DNA Resequencing ,Article ,03 medical and health sciences ,Gene Frequency ,Species Specificity ,Genotyping ,Genetics ,Molecular breeding ,Genetic diversity ,Multidisciplinary ,food and beverages ,Reference Standards ,biology.organism_classification ,Arachis hypogaea ,030104 developmental biology ,Genome, Plant ,010606 plant biology & botany ,SNP array - Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
- Published
- 2017
31. Creation of Hexaploid and Octaploid Zoysiagrass Using Colchicine and Breeding
- Author
-
Ryan N. Contreras, Scott A. Jackson, Karen R. Harris-Shultz, Christian S. Hans, and Brian M. Schwartz
- Subjects
Vegetative reproduction ,Morphological variation ,Biology ,biology.organism_classification ,chemistry.chemical_compound ,Horticulture ,chemistry ,Botany ,Colchicine ,Cultivar ,Ploidy ,Agronomy and Crop Science ,Genome size ,Zoysia - Abstract
Zoysiagrasses ( Zoysia Willd.) are a slow-grow - ing, tetraploid (2 n = 4x = 40) turfgrass that can be successfully managed with less input than many other warm-season grasses. Despite extensive genetic and morphological variation, genotypes with the ability to recuperate quickly from damage are rare. Therefore, a long-term effort to increase vegetative growth rates was initiated during 2009 by first studying the effec - tiveness of six colchicine seed treatments and breeding for manipulating the ploidy level of 'Zenith' zoysiagrass. Colchicine-treated seed - lings were screened using flow cytometry for genome size changes. Four putative octaploids and one cytochimera were identified. Average stomata length of the four colchicine-induced putative octaploids were 28% larger than that of Zenith, but the cytochimera's stomata length was not altered. p ollen diameter of the four puta - tive octaploids was larger than that of Zenith and the cytochimera. p ollen stainability was rel - atively unchanged by the colchicine treatments.
- Published
- 2013
32. The Pathogen-annotated Tracking Resource Network (PATRN) system: A web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease
- Author
-
R. Jain, Mahendra H. Kothary, M. D. Solomotis, Scott A. Jackson, Augusto A. Franco, K. Hari, M. Wekell, B. A. McCardell, Christopher J. Grim, Jayanthi Gangiredla, Joseph E. LeClerc, Gopal R. Gopinath, Atin R. Datta, Lan Hu, Michael L. Kotewicz, Venugopal Sathyamoorthy, Ben D. Tall, K. G. Jarvis, Mark K. Mammel, and Isha R. Patel
- Subjects
Food Safety ,Data management ,Information repository ,Microbiology ,Foodborne Diseases ,Data Mining ,Humans ,Cronobacter ,Information Services ,Internet ,Bacteria ,Data curation ,biology ,Information Dissemination ,business.industry ,biology.organism_classification ,Data science ,Cronobacter sakazakii ,Data aggregator ,Metadata ,Data exchange ,Food Microbiology ,Database Management Systems ,business ,Food Science - Abstract
Investigation of foodborne diseases requires the capture and analysis of time-sensitive information on microbial pathogens that is derived from multiple analytical methods and sources. The web-based Pathogen-annotated Tracking Resource Network (PATRN) system ( www.patrn.net ) was developed to address the data aggregation, analysis, and communication needs important to the global food safety community for the investigation of foodborne disease. PATRN incorporates a standard vocabulary for describing isolate metadata and provides a representational schema for a prototypic data exchange standard using a novel data loading wizard for aggregation of assay and attribution information. PATRN currently houses expert-curated, high-quality “foundational datasets” consisting of published experimental results from conventional assays and next generation analysis platforms for isolates of Escherichia coli , Listeria monocytogenes , and Salmonella , Shigella , Vibrio and Cronobacter species. A suite of computational tools for data mining, clustering, and graphical representation is available. Within PATRN, the public curated data repository is complemented by a secure private workspace for user-driven analyses, and for sharing data among collaborators. To demonstrate the data curation, loading wizard features, and analytical capabilities of PATRN, three use-case scenarios are presented. Use-case scenario one is a comparison of the distribution and prevalence of plasmid-encoded virulence factor genes among 249 Cronobacter strains with similar attributes to that of nine Cronobacter isolates from recent cases obtained between March and October, 2010–2011. To highlight PATRN's data management and trend finding tools, analysis of datasets, stored in PATRN as part of an ongoing surveillance project to identify the predominant molecular serogroups among Cronobacter sakazakii isolates observed in the USA is shown. Use-case scenario two demonstrates the secure workspace available for private users to upload and analyze sensitive data, and for collating cross-platform datasets to identify and validate congruent datapoints. SNP datasets from WGS assemblies and pan-genome microarrays are analyzed in a combinatorial fashion to determine relatedness of 33 Salmonella enterica strains to six strains collected as part of an outbreak investigation. Use-case scenario three utilizes published surveillance results that describe the incidence and sources of O157:H7 E. coli isolates associated with a produce pre-harvest surveillance study that occurred during 2002–2006. In summary, PATRN is a web-based integrated platform containing tools for the management, analysis and visualization of data about foodborne pathogens.
- Published
- 2013
33. Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions
- Author
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Jianming Yu, Shuwei Liu, Guihua Bai, Na Luo, Douglas S. Richmond, Scott A. Jackson, Ying Wang, Xiaoqing Yu, Paula M. Pijut, and Yiwei Jiang
- Subjects
Candidate gene ,Perennial plant ,Physiology ,Adaptation, Biological ,Plant Science ,drought ,Lolium perenne ,Cytosol ,Association mapping ,association mapping ,Phylogeny ,Plant Proteins ,Genetics ,education.field_of_study ,LEA3 ,biology ,food and beverages ,Chromosome Mapping ,leaf water content ,Droughts ,Phenotype ,Cyt Cu-ZnSOD ,Seeds ,FeSOD ,Antioxidant ,Research Paper ,Heterozygote ,Drought tolerance ,Population ,Molecular Sequence Data ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Quantitative trait locus ,Genes, Plant ,Polymorphism, Single Nucleotide ,Stress, Physiological ,Botany ,Lolium ,Amino Acid Sequence ,education ,Alleles ,Plant Diseases ,Superoxide Dismutase ,fungi ,Water ,biology.organism_classification ,Plant Leaves ,Amino Acid Substitution ,Mutation ,Microsatellite Repeats - Abstract
Drought is a major environmental stress limiting growth of perennial grasses in temperate regions. Plant drought tolerance is a complex trait that is controlled by multiple genes. Candidate gene association mapping provides a powerful tool for dissection of complex traits. Candidate gene association mapping of drought tolerance traits was conducted in 192 diverse perennial ryegrass (Lolium perenne L.) accessions from 43 countries. The panel showed significant variations in leaf wilting, leaf water content, canopy and air temperature difference, and chlorophyll fluorescence under well-watered and drought conditions across six environments. Analysis of 109 simple sequence repeat markers revealed five population structures in the mapping panel. A total of 2520 expression-based sequence readings were obtained for a set of candidate genes involved in antioxidant metabolism, dehydration, water movement across membranes, and signal transduction, from which 346 single nucleotide polymorphisms were identified. Significant associations were identified between a putative LpLEA3 encoding late embryogenesis abundant group 3 protein and a putative LpFeSOD encoding iron superoxide dismutase and leaf water content, as well as between a putative LpCyt Cu-ZnSOD encoding cytosolic copper-zinc superoxide dismutase and chlorophyll fluorescence under drought conditions. Four of these identified significantly associated single nucleotide polymorphisms from these three genes were also translated to amino acid substitutions in different genotypes. These results indicate that allelic variation in these genes may affect whole-plant response to drought stress in perennial ryegrass.
- Published
- 2013
34. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies
- Author
-
Junfei Zhou, Philomena Chu, Eric Lam, Hanzhong Zhang, Todd P. Michael, Weixiong Zhang, Todd C. Mockler, Boudewijn F.H. Ten Hallers, Nikolai Borisjuk, Ryan Gutierrez, Tiffany Y. Liang, Scott A. Jackson, Douglas W. Bryant, Moaine El Baidouri, Hai Peng, Alex Hastie, Jing Xia, Kenneth Acosta, Connor McEntee, and Sarah Gilbert
- Subjects
0106 biological sciences ,0301 basic medicine ,Genome evolution ,Sequence assembly ,Plant Science ,Computational biology ,Genes, Plant ,01 natural sciences ,Genome ,DNA sequencing ,Chromosomes, Plant ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genetics ,Araceae ,Genome size ,Plant Proteins ,Whole genome sequencing ,biology ,Chromosome Mapping ,Genetic Variation ,Cell Biology ,Genome project ,Sequence Analysis, DNA ,DNA Methylation ,biology.organism_classification ,030104 developmental biology ,Gene Ontology ,Spirodela ,Genome, Plant ,010606 plant biology & botany - Abstract
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.
- Published
- 2016
35. Evolution of plant genome architecture
- Author
-
Blake C. Meyers, Scott A. Jackson, Jonathan F. Wendel, and Rod A. Wing
- Subjects
0106 biological sciences ,0301 basic medicine ,Transposable element ,Arabidopsis ,Review ,Biology ,01 natural sciences ,Genome ,Evolution, Molecular ,Polyploidy ,03 medical and health sciences ,Genome Size ,Phylogenetics ,Genome size ,Phylogeny ,fungi ,food and beverages ,biology.organism_classification ,Human genetics ,030104 developmental biology ,Evolutionary biology ,DNA Transposable Elements ,Function (biology) ,Genome architecture ,Genome, Plant ,010606 plant biology & botany - Abstract
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
- Published
- 2016
36. Application of Genomic, Transcriptomic, and Metabolomic Technologies in Arachis Species
- Author
-
Jianping Wang, Ye Chu, Scott A. Jackson, Ran Hovav, Josh Clevenger, Peggy Ozias-Akins, and Brian E. Scheffler
- Subjects
Genetics ,Arachis ,Arachis ipaensis ,biology ,Genetic marker ,food and beverages ,Computational biology ,Genome project ,biology.organism_classification ,Functional genomics ,Genome ,Gene ,Arachis duranensis - Abstract
Peanut genetic improvement is approaching the cusp of rapidly accelerating gains due to application of genomic, transcriptomic, and metabolomic technologies. Yield is a primary target trait for improvement but is impacted by biotic and abiotic stresses, and quality traits specific to different cultural and industrial sectors that must be taken into account. Arachis genomic and transcriptomic resources, both for cultivated tetraploid peanut, Arachis hypogaea L., and its diploid ancestors, Arachis duranensis (A genome) and Arachis ipaensis (B genome), have been greatly enriched since their status was documented in 2012, leading to an in-depth understanding of genomic architecture based on comparative sequence analyses. Identifying genes underlying important disease resistance or quality traits requires knowledge of gene action at the level of phenotypic response as well as genetic markers within (direct) or near (indirect) genes. Once direct or indirect marker–trait linkages have been validated, markers can be used as surrogates to select for a trait. The efficacy of a marker for selection of a trait is greatest when the marker is within an identified gene; therefore, targeting gene regions for development of high-density molecular maps is desirable. The density of molecular maps in cultivated peanut has been constrained by low molecular polymorphism rates among genotypes and the limited amount of sequence data from which polymorphisms could be mined, although in spite of these limitations considerable progress has been made to develop and integrate genetic maps. The peanut genome project has generated sequence and phenotype data that vastly improve our ability to create dense genetic maps encompassing traits of interest, thereby positioning markers in or near genes with functional significance for peanut growth, productivity, and sustainability.
- Published
- 2016
37. Phylogeography of Asian wild rice,Oryza rufipogon: a genome-wide view
- Author
-
Barbara A. Schaal, Scott A. Jackson, Samara Rubinstein, Jeanmaire Molina, Michael D. Purugganan, Jonathan M. Flowers, and Pu Huang
- Subjects
Oryza sativa ,biology ,Ecology ,Range (biology) ,food and beverages ,Introgression ,biology.organism_classification ,Oryza rufipogon ,Japonica ,Sequence-tagged site ,Phylogeography ,Evolutionary biology ,Genetics ,Domestication ,Ecology, Evolution, Behavior and Systematics - Abstract
Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed.
- Published
- 2012
38. Molecular and Cytological Characterization of Centromeric Retrotransposons in a Wild Relative of Rice, Oryza granulata
- Author
-
Dongying Gao, Scott A. Jackson, Rod A. Wing, Zhiyun Gong, and Jiming Jiang
- Subjects
Comparative genomics ,Transposable element ,Genetics ,Bacterial artificial chromosome ,food and beverages ,myr ,Retrotransposon ,Plant Science ,Biology ,Oryza ,biology.organism_classification ,Genome ,Centromere - Abstract
Centromeric retrotransposons (CRs) are important component of the functional centromeres of rice chromosomes. To track the evolution of the CR elements in genus Oryza, we sequenced the orthologous region of the rice centromere 8 (Cen8) in O. granulata and analyzed transposons in this region. A total of 12 bacterial artificial chromosomes (BACs) that span the centromeric region in O. granulata were sequenced. The O. granulate centromeric sequences are composed of as much as 85% of transposons, higher than any other reported eukaryotic centromeres. Ten novel LTR retrotransposon families were identified but a single retrotransposon, Gran3, constitutes nearly 43% of the centromeric sequences. Integration times of complete LTR retrotransposons indicate that the centromeric region had a massive insertion of LTR retrotransposons within 4.5 million year (Myr), which indicates a recent expansion of the centromere in O. granulata after the radiation of the Oryza genus. Two retrotransposon families, OGRetro7 and OGRetro9, show sequence similarity with the canonical CRs from rice and maize. Both OGRetro7 and OGRetro9 are highly concentrated in the centromeres of O. granulata chromosomes. Furthermore, strong hybridization signals were detected in all Oryza species but in O. brachyantha with the OGRetro7 and OGRetro9 probes. Characterization of the centromeric retrotransposons in O. granulata confirms the conservation of the CRs in the Oryza genus and provides a resource for comparative analysis of centromeres and centromere evolution among the Oryza genus and other genomes.
- Published
- 2011
39. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
- Author
-
Guangyi Fan, Todd P. Michael, R. Varma Penmetsa, Shiaw-Pyng Yang, Reetu Tuteja, Gengyun Zhang, Rajeev K. Varshney, Rachit K. Saxena, Wei Wu, Yupeng Li, Adam M. Whaley, Bicheng Yang, Mark T.A. Donoghue, W. Richard McCombie, Charles Spillane, Jaime Sheridan, Xun Xu, Sarwar Azam, Wenbin Chen, Huanming Yang, Hari D. Upadhyaya, Scott A. Jackson, Kulbhushan Saxena, Andrew Farmer, Jessica A. Schlueter, Arvind K. Bharti, Jun Wang, Trushar Shah, Gregory D. May, Douglas R. Cook, and Aiko Iwata
- Subjects
Genetic Markers ,Chromosomes, Artificial, Bacterial ,diversification ,Sequence analysis ,Biomedical Engineering ,Bioengineering ,Genes, Plant ,Synteny ,Applied Microbiology and Biotechnology ,Genome ,l ,Cajanus ,Segmental Duplications, Genomic ,genes ,Domestication ,Gene ,database ,Repetitive Sequences, Nucleic Acid ,Segmental duplication ,Whole genome sequencing ,Bacterial artificial chromosome ,biology ,software ,business.industry ,Chromosome Mapping ,Molecular Sequence Annotation ,tool ,Sequence Analysis, DNA ,dynamics ,DNA ,families ,biology.organism_classification ,Biotechnology ,Molecular Medicine ,Soybeans ,program ,business ,Genome, Plant - Abstract
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
- Published
- 2011
40. Water, vegetation and sediment gradients in submerged aquatic vegetation mesocosms used for low-level phosphorus removal
- Author
-
Scott D. Jackson, Thomas A. DeBusk, Michelle D. Kharbanda, K. Hileman, Kevin A. Grace, and Forrest E. Dierberg
- Subjects
Aquatic Organisms ,Geologic Sediments ,Environmental Engineering ,chemistry.chemical_element ,Mesocosm ,Dry weight ,Aquatic plant ,Environmental Chemistry ,Biomass ,Muck ,Najas guadalupensis ,Waste Management and Disposal ,Environmental Restoration and Remediation ,Hydrology ,biology ,Phosphorus ,Sediment ,Ceratophyllum demersum ,Plants ,biology.organism_classification ,Pollution ,chemistry ,Wetlands ,Environmental chemistry ,Florida ,Environmental science ,Water Pollutants, Chemical ,Environmental Monitoring - Abstract
Gradients in phosphorus (P) removal and storage were investigated over 6 years using mesocosms (each consisting of three tanks in series) containing submerged aquatic vegetation (SAV) grown on muck and limerock (LR) substrates. Mean inflow total P concentrations (TP) of 32 μg L(-1) were reduced to 15 and 17 μg L(-1) in the muck and LR mesocosms, respectively. Mesocosm P loading rates (mean=1.75 gm(-2) year(-1)) varied widely during the study and were not correlated with outflow TP, which instead varied seasonally with lowest monthly mean values in December and January. The mesocosms initially were stocked with Najas guadalupensis, Ceratophyllum demersum, and Chara zeylanica, but became dominated by C. zeylanica. At the end of the study, highest vegetative biomass (1.1 and 1.4 kg m(-2) for muck and LR substrates) and tissue P content (1775 and 1160 mg kg(-1)) occurred in the first tank in series, and lowest biomass (1.0 and 0.2 kg m(-2)) and tissue P (147 and 120 mg kg(-1)) in the third tank. Sediment accretion rates (2.5, 1.9 and 0.9 cm yr(-1) on muck substrates), accrued sediment TP (378, 309 and 272 mg kg(-1)), and porewater soluble reactive P (SRP) concentrations (40, 6 and 4 μg L(-1)) in the first, second and third tanks, respectively, exhibited a similar decreasing spatial trend. Plant tissue calcium (Ca) near mesocosm inflow (19-30% dry weight) and outflow (23-26%) were not significantly different, and sediment Ca was also similar (range of 24 to 28%) among sequential tanks. Well-defined vegetation and sediment enrichment gradients developed in SAV wetlands operated under low TP conditions. While the mesocosm data did not reflect deterioration in treatment performance over 6 years, accumulation of P-enriched sediments near the inflow could eventually compromise hydraulic storage and P removal effectiveness of these shallow systems.
- Published
- 2011
41. Molecular evidence for a single evolutionary origin of domesticated rice
- Author
-
Pu Huang, Adam R. Boyko, Jeanmaire Molina, Martin Sikora, Nandita R. Garud, Carlos Bustamante, Scott A. Jackson, Samara Rubinstein, Andy Reynolds, Barbara A. Schaal, Jonathan M. Flowers, and Michael D. Purugganan
- Subjects
Multidisciplinary ,Oryza sativa ,biology ,Phylogenetic tree ,food and beverages ,Subspecies ,biology.organism_classification ,Japonica ,Coalescent theory ,Phylogenetics ,Evolutionary biology ,Botany ,Domestication ,Molecular clock - Abstract
Asian rice, Oryza sativa , is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica , were domesticated from the wild rice O. rufipogon . In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200–13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.
- Published
- 2011
42. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
- Author
-
Lincoln Stein, Dave Kudrna, Doreen Ware, Aswathy Sebastian, Bonnie L. Hurwitz, Scott A. Jackson, Andrea Zuccolo, Rod A. Wing, and Yeisoo Yu
- Subjects
Genetics ,Comparative genomics ,Genome evolution ,Oryza sativa ,biology ,food and beverages ,Cell Biology ,Plant Science ,Oryza glaberrima ,Oryza ,biology.organism_classification ,Oryza rufipogon ,Structural variation ,Oryza nivara - Abstract
Rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. Large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. We present a genome-wide study of intermediate-sized structural variation (SV) among rice (Oryza sativa) and three of its closest relatives in the genus Oryza (Oryza nivara, Oryza rufipogon and Oryza glaberrima). We computationally identified regional expansions, contractions and inversions in the Oryza species genomes relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference genome and physical maps. A subset of the computational predictions was validated using a new approach for BAC size determination. The result was a confirmed catalog of 674 expansions (25-38 Mb) and 611 (4-19 Mb) contractions, and 140 putative inversions (14-19 Mb) between the three Oryza species and O. sativa. In the expanded regions unique to O. sativa we found enrichment in transposable elements (TEs): long terminal repeats (LTRs) were randomly located across the chromosomes, and their insertion times corresponded to the date of the A genome radiation. Also, rice-expanded regions contained an over-representation of single-copy genes related to defense factors in the environment. This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery.
- Published
- 2010
43. Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum
- Author
-
Teri Rambo, Jianxin Ma, Chen Mingsheng, Rod A. Wing, Kristi Kollura, Abhijit Sanyal, Hyeran Kim, Jetty S.S. Ammiraju, Fei Lu, Phillip San Miguel, Scott A. Jackson, Jennifer Currie, Yeisoo Yu, and Jinfeng Chen
- Subjects
Chromosomes, Artificial, Bacterial ,Genome evolution ,Time Factors ,Genetic Speciation ,Molecular Sequence Data ,Locus (genetics) ,Biology ,Genes, Plant ,Oryza ,Synteny ,Genome ,Species Specificity ,Sequence Homology, Nucleic Acid ,Consensus Sequence ,Genetics ,Molecular Biology ,Gene ,Conserved Sequence ,Phylogeny ,Sorghum ,Ecology, Evolution, Behavior and Systematics ,Comparative genomics ,Oryza sativa ,Base Sequence ,Chromosomes, Artificial, P1 Bacteriophage ,Terminal Repeat Sequences ,food and beverages ,biology.organism_classification ,Diploidy ,Genetic Loci ,DNA Transposable Elements ,Databases, Nucleic Acid - Abstract
Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.
- Published
- 2010
44. The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
- Author
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Angelina Angelova, Doreen Ware, Hyeran Kim, Darshan S. Brar, Rod A. Wing, David Kudrna, Jose Luis Goicoechea, Xiang Song, Yeisoo Yu, Meizhong Luo, Nori Kurata, Nicholas Sisneros, Jetty S.S. Ammiraju, Scott A. Jackson, and Mathias Lorieux
- Subjects
Genetics ,Genome evolution ,Genetic diversity ,biology ,food and beverages ,Plant Science ,Oryza ,biology.organism_classification ,Genome ,Phylogenetics ,Genus ,Evolutionary biology ,Plant breeding ,Domestication ,Agronomy and Crop Science - Abstract
Rice was the first crop to have a high-quality reference genome sequence and is now at the forefront of intense functional and evolutionary research for two reasons-its central role in world food security, and its status as a model system for grasses. A thorough characterization of the rice genome cannot be accomplished without a deep understanding of its evolutionary history. The genus Oryza contains two cultivated and 22 wild rice species that represent 10 distinct genome types embedded within a robust phylogeny spanning a ~15 million year time span. The genus contains an untapped reservoir of agriculturally important traits and a historical record of genomic changes (especially those related to domestication, polyploidy, speciation and adaption).The two main objectives of the 'Oryza Map Alignment Project' (OMAP) were to functionally characterize the rice genome from a comparative standpoint and to provide essential tools to leverage the novel genetic diversity from wild relatives for rice improvement. The objective of this review is to summarize our efforts towards developing the most comprehensive genus-wide set of publicly available BAC resources for the genus Oryza, the first of its kind among plants (and perhaps higher eukaryotes), and their applications.
- Published
- 2010
45. A lineage-specific centromere retrotransposon in Oryza brachyantha
- Author
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Jason G. Walling, Jiming Jiang, Dongying Gao, Hyeran Kim, Chuanzhu Fan, Rod A. Wing, Ning Jiang, Jianxin Ma, Wenli Zhang, Scott A. Jackson, Navdeep Gill, Phillip SanMiguel, Yeisoo Yu, and Zhukuan Cheng
- Subjects
Genetics ,Oryza sativa ,biology ,food and beverages ,Retrotransposon ,Cell Biology ,Plant Science ,biology.organism_classification ,Oryza ,Genome ,Molecular evolution ,Centromere ,Metaviridae ,Oryza brachyantha - Abstract
Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.
- Published
- 2009
46. Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics
- Author
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Scott A. Jackson, Gregory D. May, and Steven B. Cannon
- Subjects
Crops, Agricultural ,Physiology ,Lotus japonicus ,Genomics ,Plant Science ,Genes, Plant ,Crop species ,Synteny ,digestive system ,Genome ,Focus Issue on Legume Biology ,Medicago truncatula ,Botany ,Genetics ,Translational genomics ,Trefoil ,Legume ,biology ,fungi ,food and beverages ,Sequence Analysis, DNA ,biology.organism_classification ,Lotus ,Soybeans ,Genome, Plant - Abstract
This year marks the essential completion of the genome sequences of soybean ( Glycine max ), barrel medic ( Medicago truncatula ), and birdsfoot trefoil ( Lotus japonicus ). The impact of these assembled, annotated genomes will be enormous. Birdsfoot trefoil and barrel medic, both forage crops, are
- Published
- 2009
47. Molecular and Chromosomal Evidence for Allopolyploidy in Soybean
- Author
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Jeff J. Doyle, Christian S. Hans, Seth D. Findley, Gary Stacey, Navdeep Gill, Jason G. Walling, Scott A. Jackson, and Jianxin Ma
- Subjects
Genetics ,Subfamily ,biology ,Physiology ,Satellite DNA ,Chromosome ,Plant Science ,biology.organism_classification ,Genome ,Gene duplication ,Satellite (biology) ,Glycine soja ,Segmental duplication - Abstract
Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled monomers of the two subfamilies were not detected by fluorescence in situ hybridization on extended DNA fibers nor at the sequence level. This indicates that there has been little recombination and homogenization of satellite DNA between these two sets of centromeres. These satellite repeats are also present in Glycine soja, the proposed wild progenitor of soybean, but could not be detected in any other relatives of soybean examined in this study, suggesting the rapid divergence of the centromeric satellite DNA within the Glycine genus. Together, these observations provide direct evidence, at molecular and chromosomal levels, in support of the hypothesis that the soybean genome has experienced a recent allopolyploidization event.
- Published
- 2009
48. Comparative sequence analysis of MONOCULM1 -orthologous regions in 14 Oryza genomes
- Author
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Jinfeng Chen, Yi Sui, Rentao Song, Mingsheng Chen, Antonio Costa de Oliveira, Zhukuan Cheng, Jetty S.S. Ammiraju, Fei Lu, Scott A. Jackson, Rod A. Wing, Abhijit Sanyal, Guisheng Li, Jeffrey L. Bennetzen, Xiang Song, and Shengli Zhang
- Subjects
Genetics ,Comparative genomics ,Genome evolution ,Ploidies ,Multidisciplinary ,Base Sequence ,biology ,Phylogenetic tree ,Molecular Sequence Data ,Nuclear Proteins ,food and beverages ,Oryza ,Locus (genetics) ,Genomics ,Sequence Analysis, DNA ,Biological Sciences ,Genes, Plant ,biology.organism_classification ,Genome ,Mutation ,Gene ,Genome, Plant - Abstract
Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza , this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 ( MOC1 ) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.
- Published
- 2009
49. Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean
- Author
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Carine Ameline-Torregrosa, Roxanne Denny, Majesta O'Bleness, Ashley Nguyen, Roger W. Innes, Sue Sherman-Broyles, Béatrice Segurens, Jeff J. Doyle, Jing Yi, Christian S. Hans, Valérie Geffroy, Hongshing Lai, Stacy Howell, Michelle Metcalf, Adam Wawrzynski, Anita Dalwani, Nicolas W.G. Chen, Ethalinda K. S. Cannon, Ben Chacko, Arnaud Couloux, Tom Ashfield, Scott A. Jackson, Nevin D. Young, Milind B. Ratnaparkhe, Daniel C. Ilut, Sylvie Samain, Jafar Mammadov, Bruce A. Roe, Bernard E. Pfeil, Shweta Deshpande, Ram Podicheti, Mireille Sévignac, Natasha Glover, Ashley N. Egan, Steven B. Cannon, Sara E. Martin del Campo, M. A. Saghai Maroof, Jason G. Walling, Iryna Sanders, Dominic M. Tucker, and Vincent Thareau
- Subjects
Chromosomes, Artificial, Bacterial ,DNA, Plant ,Retroelements ,Physiology ,Centromere ,Retrotransposon ,Plant Science ,Plant disease resistance ,Biology ,Genes, Plant ,Genome ,Evolution, Molecular ,Polyploidy ,Gene Duplication ,Genotype ,Genetics ,Gene ,Phylogeny ,Plant Diseases ,Phaseolus ,food and beverages ,myr ,Sequence Analysis, DNA ,Genome Analysis ,biology.organism_classification ,Immunity, Innate ,Medicago truncatula ,Mutagenesis, Insertional ,Multigene Family ,Soybeans ,Gene Deletion ,Genome, Plant - Abstract
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
- Published
- 2008
50. Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana
- Author
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Scott A. Jackson, Jessica A. Schlueter, Randy C. Shoemaker, and Brian E. Scheffler
- Subjects
Arabidopsis ,Biology ,Genes, Plant ,Synteny ,Genome ,Evolution, Molecular ,Gene Duplication ,Medicago truncatula ,Gene cluster ,Genetics ,Arabidopsis thaliana ,Molecular Biology ,Gene ,Phylogeny ,Genetics (clinical) ,Bacterial artificial chromosome ,Genetic Variation ,food and beverages ,biology.organism_classification ,Tandem Repeat Sequences ,Soybeans ,Tandem exon duplication ,Acyltransferases ,Genome, Plant ,Biotechnology - Abstract
Extended comparison of gene sequences found on homeologous soybean Bacterial Artificial Chromosomes to Medicago truncatula and Arabidopsis thaliana genomic sequences demonstrated a network of synteny within conserved regions interrupted by gene addition and/or deletions. Consolidation of gene order among all 3 species provides a picture of ancestral gene order. The observation supports a genome history of fractionation resulting from gene loss/addition and rearrangement. In all 3 species, clusters of N-hydroxycinnamoyl/benzoyltransferase genes were identified in tandemly duplicated clusters. Parsimony-based gene trees suggest that the genes within the arrays have independently undergone tandem duplication in each species.
- Published
- 2008
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