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Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.

Background The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. Results Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. Conclusions The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop. Electronic supplementary material The online version of this article (10.1186/s12864-019-5734-x) contains supplementary material, which is available to authorized users.

Summary Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented., Significance Statement State‐of‐the‐art technologies and assembly methods were used to generate a reference genome sequence of cowpea, a drought‐resilient crop on which millions of people in sub‐Saharan Africa depend as a source of protein. This sequence facilitated the identification of: repetitive elements and gene families expanded in cowpea compared with other closely related legumes; a large and apparently rare chromosomal inversion; and an interesting candidate gene that is associated with several domestication‐related traits.

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Figure S2. Sugar accumulation in the topmost internode over time in the Rio and PR22 genotypes. Sugar is measured as Brix (soluble sugar concentration) in 3 biological replicates of each genotype at each of the 5 developmental time points used for the RNA seq analysis. The same plants were used for both Brix measurements and RNA material collection. (PDF 98 kb)

Additional file 1: Supplementary Methods: Sequencing, genome assembly and construction of pseudomolecule chromosomes, and BAC library construction. Table S1. Genomic libraries included in the Oryza sativa (KitaakeX) genome assembly and their respective assembled sequence coverage levels in the final release. Table S2. PACBIO library statistics for single pass yield of the 42 chips included in the Oryza sativa (KitaakeX) genome assembly and their respective assembled sequence coverage levels. Table S3. Summary statistics of the output of the SuperNova whole genome shotgun assembly prior to integration with the PACBIO assembly. Table S4. Summary statistics of the raw output of the MECAT whole genome shotgun assembly. Figure S1-S12. Syntenic Japonica sequence placements on the Oryza sativa (var. KitaakeX) chromosomes. Each figure shows one chromosome. Table S5. Final summary assembly statistics for chromosome scale assembly Figure S13. Dot plot of BAC clone 119,492 on a region of Chr_02. Figure S14. Dot plot of BAC clone 120,743 on a region of Chr_12. Figure S15. Dot plot of BAC clone 119,503 in a region of Chr_06. Table S6. KitaakeX BAC libraries used for genome assembly and construction of pseudomolecule chromosomes. For Figures S1-S12, plot of the marker placements for each chromosome is shown.

Figure S1. Frequency distributions of structural variants predicted by Assemblytics (based on Nucmer alignment of Rio and BTx623). In this analysis, BTx623 is the reference genome, so events such as insertions and deletions have occurred in Rio with respect to BTx623. (PDF 13 kb)

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.

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks., Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

© 2018, Filiault et al. The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

Author(s): Filiault, D; Ballerini, E; Mandakova, T; Akoz, G; Derieg, N; Schmutz, J; Jenkins, J; Grimwood, J; Shu, S; Hayes, R; Hellsten, U; Barry, K; Yan, J; Mihaltcheva, S; Karafiatova, M; Nizhynska, V; Lysak, M; Hodges, S; Nordborg, M | Abstract: The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea "Goldsmith", complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analysis reveals extensive allele sharing among species, and sheds light on the complex process of radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differed from that of the rest of the genome --- a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

et al., The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes., The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Support to RR and SAR by the German Research Foundation (DFG RE 837/10-2), the Excellence Initiative of the German Federal and State Governments (EXC 294), and by the German Federal Ministry of Education and Research (BMBF FRISYS), is highly appreciated. CoGe is supported by the US National Science Foundation under Award Numbers IOS-339156 and IOS-1444490, CyVerse is supported by the U.S. National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383. YK and ACC are grateful for support from the UK Biological Sciences and Biotechnology Research Council (Grant BB/F001797/1). KV acknowledges the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project (no 01MR0410W) of Ghent University. JC is grateful for support from the Spanish Ministerio de Economía y Competitividad (Grant AGL2013-43244-R). RSQ is grateful to Monsanto (St. Louis, MO, USA) for sequencing genomic DNA of P. patens accession Kaskaskia. The 1000 Plants (1 KP) initiative, led by GKSW, is funded by the Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB). TW was supported by EMBO Long-Term Fellowships (ALTF 1166-2011) and by Marie Curie Actions (European Commission EMBOCOFUND2010, GA-2010-267146). The work conducted at PGSB was supported by the German Research Foundation (SFB924) and German Ministry of Education and Research (BMBF, 031A536/de.NBI).

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops., Crassulacean acid metabolism (CAM) is a metabolic adaptation of photosynthesis that enhances water use efficiency. Here, via genomic analysis of Kalanchoë, the authors provide evidence for convergent evolution of protein sequence and temporal gene expression underpinning the multiple independent emergences of CAM.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant., 陸上植物の祖先の特徴をもつ苔類ゼニゴケの全ゲノム構造を解明. 京都大学プレスリリース. 2017-10-06.

Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-Tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.

Fossil evidence shows that red algae (Rhodophyta) are one of the most ancient multicellular lineages. Their ecological, evolutionary, and commercial importance notwithstanding, few red algal nuclear genomes have been sequenced. Our analyses of the Porphyra umbilicalis genome provide insights into how this macrophyte thrives in the stressful intertidal zone and into the basis for its nutritional value as human food. Many of the novel traits (e.g., cytoskeletal organization, calcium signaling pathways) we find encoded in the Porphyra genome are extended to other red algal genomes, and our unexpected findings offer a potential explanation for why the red algae are constrained to small stature relative to other multicellular lineages.

Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B. braunii will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism.

Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B. braunii will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

2ABSTRACTSorghum bicoloris a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.

MareyMap plot of TxE linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 236Â kb)

Background The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Results Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. Conclusions The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3606-9) contains supplementary material, which is available to authorized users.

Anchoring of the peach scaffolds to the three genetic maps. Colored bars represent the 8 linkage groups: pink for PxF, purple for TxE and blue for CxA. WGS scaffolds were positioned in each pseudomolecule (Pp01 to Pp08) with the corresponding genetic markers and are depicted in three different colors (dark blue, pink and pale blue); genetic markers are in the same colors of the corresponding WGS scaffolds. The zero (0) denotes the six scaffolds placed with random orientation along the pseudomolecules. The asterisk (*) indicates the two scaffolds with random order. The crosshatch (#) indicates the two scaffolds with the wrong order in Peach v2.0 that need to be inverted in a future release. (PDF 495Â kb)

MareyMap plot of CxA linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 233Â kb)

MareyMap plot of PxF linkage maps (including the F1 and recurrent parent maps). Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 405Â kb)

The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

SummaryGenome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.PaperClip

PCR validation of SNPs identified between ‘Alamo’ and ‘Dacotah’ using conserved primers. Figure S2 contains sequencing and alignment data from PCR validation of SNPs identified between ‘Alamo’ and ‘Dacotah’ using conserved primers. The SNP locations predicted by RNA-seq have been highlighted in yellow. (DOCX 25 kb)

Labeled phylogenetic tree of 578 switchgrass RGHs and 116 Brachypodium distachyon RGHs. Figure S1 is a replica of the phylogenetic tree included in the paper but it contains the IDs of the 578 switchgrass RGHs and 116 Brachypodium distachyon RGHs. (PDF 820 kb)

Motivation: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Results: Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. Availability: GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License ( http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org). Contact:cjm@fruitfly.org or emmert@morgan.harvard.edu.

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains “islands” of highly conserved genes embedded in these “oceans” of complex repeats, which may require special expression and splicing mechanisms.

Five years after the completion of the sequence of the Drosophila melanogaster genome, the number of protein-coding genes it contains remains a matter of debate; the number of computational gene predictions greatly exceeds the number of validated gene annotations. We have assembled a collection of >10,000 gene predictions that do not overlap existing gene annotations and have developed a process for their validation that allows us to efficiently prioritize and experimentally validate predictions from various sources by sequencing RT-PCR products to confirm gene structures. Our data provide experimental evidence for 122 protein-coding genes. Our analyses suggest that the entire collection of predictions contains only ≈700 additional protein-coding genes. Although we cannot rule out the discovery of genes with unusual features that make them refractory to existing methods, our results suggest that the D. melanogaster genome contains ≈14,000 protein-coding genes.

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosophila species.

The role of semiochemicals in host location by the parasitoid Pteromalus cerealellae (Boucek) was investigated in Y-tube and three-way olfactometers, by measuring responses to stimuli associated with the cowpea weevil, Callosobruchus maculatus. Orientation of mated parasitoid females was measured in response to five stimuli: live virgin female bruchid beetles, solvent extracts of whole body virgin female bruchids, solvent extracts of the oviposition marking pheromone from a glass substrate, previously infested cowpea seeds with adult emergence holes, and uninfested cowpea seeds. All stimuli elicited significantly better responses than those to blank controls. Female parasitoids that had previous exposure to live, virgin beetles and infested seeds exhibited shorter latency and response times to the stimuli than did naive females. Live, virgin female bruchids and whole body solvent extracts of virgin female bruchids elicited the strongest responses. Comparison of responses in a three-way olfactomet...

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.

Olanzapine is a second generation antipsychotic. A common side effect in humans is weight gain, but the mechanisms are mostly unknown.To study the effects of subchronic olanzapine treatment on body weight, fasting plasma glucose (FPG), fasting insulin (FINS), C-peptide, insulin sensitivity index (ISI), and expression of glucose transporter 2 (GLUT2) in rat pancreatic β cells.Female Sprague-Dawley rats were randomly divided into two groups: the olanzapine-treated group and the control group (each n = 8). Rats in the olanzapine-treated group intragastrically received olanzapine 5 mg/kg/day for 28 days; the rats in the control group received the same volume of vehicle. FPG and body weight were measured on the 1st, 7th, 14th and 28th day. FINS and C-peptide were measured using immunoradiometric assays at baseline and on the 28th day. GLUT2 mRNA and protein expressions in pancreatic β cells were analyzed by RT-PCR and western blot.Olanzapine-treated rats had higher body weight (227.4 ± 8.9 vs. 211.0 ± 9.9 g), FPG (5.86 ± 0.42 vs. 4.24 ± 0.29 mmol/L), FINS (17.34 ± 3.64 vs. 10.20 ± 1.50 µIU/mL), and C-peptide (0.154 ± 0.027 vs. 0.096 ± 0.009 ng/mL) than those in controls (all P0.05) at the 28th day. Pancreatic β cells of the olanzapine-treated group showed lower ISI (-4.60 ± 0.23 vs. -3.76 ± 0.20) and GLUT2 levels (mRNA: 1.12 ± 0.02 vs. 2.00 ± 0.03; protein: 0.884 ± 0.134 vs. 1.118 ± 0.221) than those in controls (all P0.05).Subchronic olanzapine treatment inhibited expression of GLUT2 in rat pancreatic β cells. Therefore, it may disturb glucose metabolism via the insulin resistance of β cells, but confirmation in humans is needed.

Reproductive characteristics of a northeastern Kansas population of the fritillary Speyeria idalia (Drury) were studied. Hemolymph juvenile hormone (JH) titers, ovarian development, and fat body utilization were monitored weekly in adult females over their entire 1997 flight period, which extended from mid-June to early October. Dissections of female reproductive systems revealed that S. idalia females mate just once, soon after they emerge in mid- to late June. Gas chromatographic-mass spectrometric determinations of juvenile hormone suggested that they undergo a reproductive diapause through mid-August related to the absence of or very low titers of juvenile hormone. Oogenesis and fat body depletion do not commence until late August/early September, soon after which oviposition occurs. The onset of oogenesis coincides with a rapid rise in hemolymph titers of JH I, JH II, and JH III. The predominant juvenile hormone homolog was JH II, but both JH I and JH III exhibited smaller, concomitant peaks. Four fundamentally different lepidopteran reproductive strategies have been recognized based on various reproductive characteristics and the type of gonadotropic hormones used to stimulate oogenesis. Speyeria idalia exhibits a type of reproductive strategy that has not been documented in Lepidoptera, typified by protandry, female monandry, long-lived (>8 wk) females that feed throughout their adult lives, greatly delayed oogenesis that occurs late in adult life, and apparent juvenile hormone control of gonadotropic processes. This reproductive strategy appears to be an adaptation to the phenology of larval host plants, namely coordinating the life cycle with that of the seasonally restricted violets on which larval survival of this monophagous species depends.

Females of Callosobruchus spp. are known to produce sex pheromones that attract males. These sex pheromones cannot be adopted for use in pest management without first investigating the responses of the males in the windless conditions of storage environments. Consequently, behavioural bioassays of Callosobruchus subinnotatus Pic males were conducted in an olfactometer in the absence of air-flow. Under these conditions males were found to be able to follow odour trails to the source. However, the latency period was longer in diffusional bioassays than for insects in a Y-tube olfactometer that provided directional wind cues. The highest percentage of males reached the pheromone source when components of the pheromones, (E)-3-methyl-2-heptenoic acid (E32A) and (Z)-3-methyl-2-heptenoic acid (Z32A), were formulated in a 50:50 or 25:75 ratio. Males of C. maculatus (Fabricius) responded to sex pheromone of C. subinnotatus, but males of C. subinnotatus did not respond to that of C. maculatus. The two sex pheromone components of C. subinnotatus are also constituents of C. maculatus sex pheromone. These two components may be potentially useful in monitoring the populations of both species in stored beans. It is postulated that (Z)-3-methyl-3-heptenoic acid (Z33A), the major component of the sex pheromone of C. maculatus, must have acted as an antagonist inhibiting response of C. subinnotatus to the sex pheromone of C. maculatus.

Vitellogenin (Vg) concentration was determined in pupal hemolymph of female southwestern corn borer, Diatraea grandiosella (Dyar). Vitellogenin concentration increased significantly with pupal age. Vitellogenin level reached 7 mg/ml on day 7 after pupation. The vitellogenin was separable into 2 apoproteins on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), with molecular weights of 145,000 for apoVg-I and 38,000 for apoVg-II. SDS-PAGE analysis revealed that vitellogenin polypetides in female pupal hemolymph appeared to be identical to those from eggs, but were absent in male and early female pupal hemolymph. A method to quantify vitellogenin by indirect ELISA is described. Results from this study and those of a previous study suggest that juvenile hormone does not have a role in vitellogenesis but does so in choriogenesis.

Rearing of Callosobruchus subinnotatus (Pic) under crowded condition at 30°C and 80% RH produced active males and females. The active individuals emerged later than normal individuals and were lighter in weight. The responses of normal and active males of C. subinnotatus to sex pheromone were compared in electroantennogram (EAG) and olfactometry bioassays. The olfactometry bioassay involved observing males in Y-tubes containing blends of the components of the sex pheromone in one arm and a blank filter paper in the other. Behavioral characteristics of males were analyzed as they walked upwind in the tubes. The latency periods were shorter in active than in normal males. More normal males reached the source and spent more time on the source compared with active males. The normal males clearly demonstrated preference for 2 blends of the sex pheromone containing the (E)-3-methyl-2-heptenoic acid (E32C7) and (Z)-3-methyl-2-heptenoic acid (Z32C7) isomers in the ratio of 75%:25% and 50%:50%, whereas active males showed preference for blends comprising >50% of the Z isomer. The EAG bioassay showed that responses of normal males to female pheromone extracts were twice those of active males.

Sex pheromone produced by Callosobruchus subinnotatus females stimulates conspecific males to walk upwind toward the source. Gas chromatographic and mass spectrometric analyses of sex pheromone components and their hydrogenated derivatives suggested that the sex pheromone consisted of two short-chain fatty acids, (E)-3-methyl-2-heptenoic acid (E32C7) and (Z)-3-methyl-2-heptenoic acid (Z32C7). The composition of the sex pheromone was confirmed by electrophysiological and behavioral bioassays with synthetic compounds. A mixture of 5 ng E32C7 and 5 ng Z32C7 elicited a 2.1-mV male EAG response, whereas the solvent control elicited 0.1 mV. Mixtures of the two compounds at various ratios were attractive to males in Y-tube bioassays. A pitfall-type trap equipped with a lure impregnated with 1 ng E32C7 and 1 ng Z32C7 was effective in trapping males. Traps baited with the lure caught 80% of males in a glass aquarium during nighttime and 50% during daytime, whereas control traps (solvent treated) in a separate aquarium caught 20% and 10%, respectively.

Factors affecting sex pheromone production and male responses in the bruchid beetle, Callosobruchus subinnotatus (Pic), were studied using electroantennogram (EAG) and behavior assays. Virgin females at emergence already had produced a significant amount of putative sex pheromone. As females grew older, sex pheromone production reached a maximum at age 2 d. Virgin females emitted pheromone throughout the day, but they emitted slightly less during the 2nd half of photophase. Immediately after mating, females produced significantly less sex pheromone than did virgin females of the same age, but older mated females produced similar amounts of pheromone to those of virgin females of the same age. The pygidium is the likely site of sex pheromone production, because extracts of pygidium elicited highest male EAG responses among the extracts of various dissected body parts of newly emerged females. Male EAG responses increased with the male age.

Studies were undertaken to determine whether adult males of Heliothis virescens transfer juvenile hormone (JH) to females during copulation, and an in vitro radiochemical assay was used to determine whether mating causes an allatotropic effect, i.e., stimulation of JH biosynthesis by corpora allata (CA). In vitro, CA from 3-day-old mated females synthesized and released approximately 2.5 times total JH as that of CA from comparably aged virgin females. Of the homologues, JH II exhibited significant increase in mated females; JH I also increased but not significantly. JH III remained similar to that of virgin females. This is the first demonstration of an allatotropic effect of mating in moths. In contrast to the female, CA of virgin males did not produce any JH, but accessory sex glands (ASG) in 3-day-old males synthesized small amounts of JH. Immediately after adult emergence, male ASG contained approximately 1.5 ng JH I and II, which increased by 12 h after emergence and remained at this high level up to 54 h after emergence. JH III was barely detected in ASG. JH in ASG of mated male immediately after uncoupling was depleted almost completely, and 24 h later recovered to levels comparable to that of 54-h-old virgin male. Virgin female bursa copulatrix did not contain any JH, but mated female bursa, immediately after uncoupling, had JH at levels comparable to that observed in virgin male ASG. By 6 h after uncoupling, JH levels decreased dramatically in mated female bursa. These data suggest the transfer of JH to females by the male.

Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users., Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users.

Juvenile hormones I, II and III were monitored in hemolymph of pupal and adult stages of various ages of Diatraea grandiosella females. JH III was the predominant homologue followed by JH II, and JH I was rarely detectable. At day 5 after pupation, no JH was detectable. JH titers increased from 7.5 days after pupation to a peak of 24.8 ng ml −1 JH II and 26 ng ml −1 JH III at adult emergence and then declined to low levels by 24 h after emergence. Ovarian development in D. grandiosella parallels changes in hemolymph JH titers, but the role of JH in vitellogenesis is unclear since the time of vitellogenesis initiation has yet to be determined. No apparent vitellogenin deposition was observed in eggs 5 days after pupation. Some oocytes were partially vitellogenic by 7.5 days after pupation and oocytes continued to grow afterwards, but no oocytes were chorionated during the pupal stage. Chorionated oocytes were observed in 24-h-old female moths. Juvenile hormone is essential for chorion formation in this species, because decapitated pupae treated with 10 μ g JH III in corn oil developed chorionated oocytes while decapitated pupae treated with corn oil did not.

Mating and oviposition behaviors were studied inCallosobruchus subinnotatus. Copulation was most frequent during the late scotophase, 2–3 h before onset of photophase. The females were less willing to mate during photophase, which increased the time to initiate mating while decreasing the duration of mating. Females exhibited increased movement prior to mating, resting immediately after mating, and remained stationary for 6 h when oviposition commenced. Multiple mating by both males and females affected the number of eggs laid, duration of mating, and uncoupling time at the end of mating. Females that mated two or three times laid more eggs than females that mated once or more than three times. Females that remainedin copula for less than 18 min showed greater readiness to remate than those that remainedin copula longer. There was a gradual decrease in the number of eggs females could lay with an increase in the number of previous matings by males.

The characteristics of vitellogenin (Vg) and the relationship between Vg production and egg production in the tobacco budworm, Heliothis virescens, were studied. The relationship between Vg production and juvenile hormone (JH) and the impact of mating on Vg and egg production were also investigated. Vg appears in the hemolymph of H. virescens about 6 h after moth eclosion. Vg may be separated into two apoproteins (ApoVg-I and ApoVg-II) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weights were calculated to be 156,065 ± 800 for ApoVg-I and 39,887 ± 323 for ApoVg-II. SDS-PAGE analysis revealed that the female hemolymph Vg polypeptides appear to be identical to those from eggs but are absent in male hemolymph. Vg concentration was significantly higher in mated females than in virgin females of the same age at 48 h after emergence. Rates of egg production increased as Vg production increased; rates of egg production in mated females were significantly higher than those of virgin females at 48, 72, 96, and 120 h postemergence. Vg production is dependent on JH, because hemolymph from decapitated females lacked Vg while that of decapitated females treated with synthetic JH had Vg at levels comparable to similarly aged, normal H. virescens females. Hemolymph JH titers in mated females were significantly higher compared with those in virgin females at all sampling periods. The high JH level in mated females may explain the high Vg and egg production in mated H. virescens. Arch. Insect Biochem. Physiol. 34:287–300, 1997. © 1997 Wiley-Liss, Inc.