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68. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Author

Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi

Published
2009

69. La contribution de Jean-Frédéric ChaiUet à l'œuvre botanique de Jean Gaudin.

Author

DI MAIO, Edouard, VUST, Mathias, and GRANT, Jason R.

Abstract

Copyright of Bulletin de la Societe Vaudoise des Sciences Naturelles is the property of Societe Vaudoise des Sciences Naturelles and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2022
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75. Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation

Author

Tsoi Stephen, Zhou Chi, Grant Jason R, Pasternak J, Dobrinsky John, Rigault Philippe, Nieminen Julie, Sirard Marc-André, Robert Claude, Foxcroft George R, and Dyck Michael K

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The domestic pig is an important livestock species and there is strong interest in the factors that affect the development of viable embryos and offspring in this species. A limited understanding of the molecular mechanisms involved in early embryonic development has inhibited our ability to fully elucidate these factors. Next generation deep sequencing and microarray technologies are powerful tools for delineation of molecular pathways involved in the developing embryo. Results Here we present the development of a porcine-embryo-specific microarray platform created from a large expressed sequence tag (EST) analysis generated by Roche/454 next-generation sequencing of cDNAs constructed from critical stages of in vivo or in vitro porcine preimplantation embryos. Two cDNA libraries constructed from in vitro and in vivo produced preimplantation porcine embryos were normalized and sequenced using 454 Titanium pyrosequencing technology. Over one million high-quality EST sequences were obtained and used to develop the EMbryogene Porcine Version 1 (EMPV1) microarray composed of 43,795 probes. Based on an initial probe sequence annotation, the EMPV1 features 17,409 protein-coding, 473 pseudogenes, 46 retrotransposed, 2,359 non-coding RNA, 4,121 splice variants in 2,862 genes and a total of 12,324 Novel Transcript Regions (NTR). After re-annotation, the total unique genes increased from 11,961 to 16,281 and 1.9% of them belonged to a large olfactory receptor (OR) gene family. Quality control on the EMPV1 was performed and revealed an even distribution of ten clusters of spiked-in control spots and array to array (dye-swap) correlation was 0.97. Conclusions Using next-generation deep sequencing we have produced a large EST dataset to allow for the selection of probe sequences for the development of the EMPV1 microarray platform. The quality of this embryo-specific array was confirmed with a high-level of reproducibility using current Agilent microarray technology. With more than an estimated 20,000 unique genes represented on the EMPV1, this platform will provide the foundation for future research into the in vivo and in vitro factors that affect the viability of porcine embryos, as well as the effects of these factors on the live offspring that result from these embryos.

Published
2012
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76. Comparing thousands of circular genomes using the CGView Comparison Tool

Author

Grant Jason R, Arantes Adriano S, and Stothard Paul

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the biology and evolution of the source organism. Visualization of the results is important, as it allows information from a variety of sources to be integrated and interpreted. However, existing graphical comparison tools lack features needed for efficiently comparing a new genome to hundreds or thousands of existing sequences. Moreover, existing tools are limited in terms of the types of comparisons that can be performed, the extent to which the output can be customized, and the ease with which the entire process can be automated. Results The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation. Conclusion CCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/.

Published
2012
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78. A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

Author

Tantia Madhu S, Galvão Stephan R, Caetano Alexandre R, Mariani Paola, Miziara Melissa N, Kumar M Aravind, Mathew Boby, Saradhi G Pardha, Kumar Satish, Prasad Aparna, Lin Guohui, Cai Zhipeng, Jeong Jooha, Greco Anthony J, Kochan Kelli J, Brunner Ronald M, Weikard Rosemarie, Goldammer Tom, Filho Edson, Stafuzza Nedenia B, Riggs Penny K, Grant Jason R, Amaral M Elisabete J, Vijh Ramesh K, Mishra Bina, Kumar ST Bharani, Pelai Vanderlei A, Santana Andre M, Fornitano Larissa C, Jones Brittany C, Tonhati Humberto, Moore Stephen, Stothard Paul, and Womack James E

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. Results A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). Conclusion We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

Published
2008
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79. Two new species of Gentianella (Gentianaceae) from Peru

Author

Pringle, James S and Grant, Jason R

Abstract

Two new species of Gentianella (Gentianaceae, Gentianeae, Swertiinae), G. grantii and G. wayqecha, are described from Departamento Cusco, Peru. These two species differ from other Peruvian species of Gentianella in a combination of stems 10–100 cm long; no rosette of basal leaves; cauline leaves 10– 75 mm long; flowers in thyrses; and corollas 14–26 mm long, campanulate, and adaxially glabrous. The leaves of G. grantii consist of an appressed pseudopetiole and a spreading, narrowly elliptic-oblong to linear blade; the corollas are lavender; and the corolla lobes are 0.6–0.7× as long as the tube. Gentianella grantii is similar to G. lythroides, of Bolivia, but differs in having more closely spaced leaves and less deeply lobed corollas. The leaves of G. wayqecha are sessile, lanceolate to ovate; the corollas are rose-violet; and the corolla lobes are 0.75–1.35× as long as the tube. Gentianella wayqecha is similar to G. rapunculoides, of Colombia and Ecuador, and G. ruizii, of Peru, but differs from both in its adaxially glabrous corollas and from G. rapunculoides in its less deeply lobed corollas. Both G. grantii and G. wayqecha grow in moist habitats near tree line, and are known only from a area northeast of the city of Cusco.

Published
2017

80. Andean Speciation and Vicariance in Neotropical Macrocarpaea (Gentianaceae-Helieae)

Author

Struwe, Lena, Haag, Scott, Heiberg, Einar, and Grant, Jason R

Abstract

The genus Macrocarpaea (Griseb.) Gilg (Gentianaceae, Helieae) is among the largest woody genera of tropical gentians, with most of its species occurring in the wet mountainous forests of the Andes. Phylogenetic and dispersal-vicariance analyses (DIVA) of 57 of the 105 currently recognized species in the genus, using two data sets from nuclear DNA (ITS and 5S-NTS sequences) and morphology, show a single origin of the Andean species from an ancestral distribution that includes southeastern Brazil. Within the Andes, species divide into two major clades: (1) northern species from the cordilleras of northern Ecuador, Colombia, and Venezuela; and (2) southern species of the Andean Amotape–Huancabamba Zone in Ecuador and Peru, as well as the Andes of central and southern Peru and Bolivia. The Amotape–Huancabamba Zone is supported as the ancestral area for Macrocarpaea within the Andes. There are repeated speciation patterns within the Andes, and three Mesoamerican species derive from the northern clade, as is the single sampled species from the Guayana Shield. The position of the subclade of the three Caribbean species is less certain, but it currently nests among Andean species. An Atlantic coastal Brazilian clade is placed as sister group to all other Macrocarpaea, providing further support for an ancestral refuge in southeastern Brazil for the Helieae. The biogeographic analysis showed that local speciation is more common than long-distance dispersal, and allopatric speciation is more common than sympatric speciation. Using detailed, georeferenced herbarium collection data, patterns in environmental characteristics between clades and sister species were analyzed with Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), utilizing geographic information system (GIS) and statistical methods. Sister clades and taxa were evaluated for statistical significance in variables such as annual rainfall and temperature, elevation, temperature and rainfall seasonality, geological bedrock age, and soil type to evaluate ecological vicariance between sister groups. The results indicate that there are no general patterns for each variable, but that there are many significant divergences in ecological niches between both larger sister groups and sister species, and ecological niche conservation was also observed when subsequent nodes in the phylogeny were compared.

Published
2017

81. Molecular phylogenetics supports widespread cryptic species in moonworts (Botrychium s.s., Ophioglossaceae)

Author

Dauphin, Benjamin, Vieu, Julien, and Grant, Jason R

Abstract

Premise of the study: Previous phylogenetic studies of moonworts (Botrychium sensu stricto (s.s.)) included few taxa from outside of North America. This low geographical representation limited interpretations of relationships of this group rich in cryptic species. With 18 out of 30 species in the genus being polyploid, understanding their evolutionary history remains a major challenge. Methods: A new molecular phylogeny was reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI) analyses based on multiple accessions of the most wide- ranging Arctic taxa of Botrychium in North America and Europe using three noncoding plastid DNA regions (psbA-trnHGUG, trnLUAA- trnFGAA intergenic spacer, and rpL16 intron). Key results: The new phylogeny confirms the identity of several recently described species and proposed new taxa. Nine subclades are newly identified within the two major clades in Botrychium s.s.: Lanceolatum and Lunaria. Chloroplast DNA was variable enough to separate morphologically cryptic species in the Lunaria clade. On the contrary, much less variation is seen within the morphologically variable Lanceolatum clade despite sampling over the same broad geographic range. The chloroplast region psbA-trnHGUG is identified as an efficient DNA barcode for the identification of cryptic taxa in Botrychium s.s. Conclusions: The combined increase in species representation, samples from throughout the geographic range of each species, and sequencing of multiple plastid DNA regions supports morphologically cryptic species in Botrychium s.s.

Published
2017

83. Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae).

Author

Sandoz, Frédéric Alexandre, Bindschedler, Saskia, Dauphin, Benjamin, Farinelli, Laurent, Grant, Jason R., and Hervé, Vincent

Subjects
FUNGAL communities, PLANT-fungus relationships, ECTOMYCORRHIZAS, VESICULAR-arbuscular mycorrhizas, FERNS, GENETIC barcoding
Abstract

Summary: Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co‐occurrence analyses, suggesting a role for fungus–fungus interactions in AMF community assembly. In particular, OTU co‐occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands. [ABSTRACT FROM AUTHOR]

Published
2020
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85. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data

Author

Schober, Daniel, primary, Jacob, Daniel, additional, Wilson, Michael, additional, Cruz, Joseph A., additional, Marcu, Ana, additional, Grant, Jason R., additional, Moing, Annick, additional, Deborde, Catherine, additional, de Figueiredo, Luis F., additional, Haug, Kenneth, additional, Rocca-Serra, Philippe, additional, Easton, John, additional, Ebbels, Timothy M. D., additional, Hao, Jie, additional, Ludwig, Christian, additional, Günther, Ulrich L., additional, Rosato, Antonio, additional, Klein, Matthias S., additional, Lewis, Ian A., additional, Luchinat, Claudio, additional, Jones, Andrew R., additional, Grauslys, Arturas, additional, Larralde, Martin, additional, Yokochi, Masashi, additional, Kobayashi, Naohiro, additional, Porzel, Andrea, additional, Griffin, Julian L., additional, Viant, Mark R., additional, Wishart, David S., additional, Steinbeck, Christoph, additional, Salek, Reza M., additional, and Neumann, Steffen, additional

Published
2017
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86. A community-derived classification for extant lycophytes and ferns

Author

Pteridophyte Phylogeny Group, The, Schuettpelz, Eric, Schneider, Harald, Smith, Alan R, Hovenkamp, Peter, Prado, Jefferson, Rouhan, Germinal, Salino, Alexandre, Sundue, Michael, Almeida, Thaís Elias, Parris, Barbara, Sessa, Emily B, FIeld, Ashley R, de Gasper, André Luís, Rothfels, Carl J, Windham, Michael D, Lehnert, Marcus, Dauphin, Benjamin, Ebihara, Atsushi, Lehtonen, Samuli, Schwartsburd, Pedro Bond, Metzgar, Jordan, Zhang, L-Bing, Kuo, Li-Yaung, Brownsey, Patrick J, Kato, Masahiro, Arana, Marcelo Daniel, Assis, Francince C, Barker, Michael S, Barrington, David S, Chang, Ho-Ming, Chang, Yi-Han, Chao, Yi-Shan, Chen, Cheng-Wei, Chen, De-Kui, Chiou, Wen-Liang, Dittrich, Jose María Gabriel, Duan, Yi-Fan, Dubuisson, Jean-Yves, Farrar, Donald R, Fawcett, Susan, Galán, Jose María Gabriel y, Góes-Neto, Luiz Armando de Araújo, Grant, Jason R, Grusz, Amanda L, Haufler, Christopher, Hauk, Warren, He, Hai, Hennequin, Sabine, Hirai, Regina Yoshie, Huiet, Layne, Kessler, Michael, Korall, Petra, Labiak, Paulo H, Larsson, Anders, León, Blanca, Li, Chun-Xiang, Li, Fay-Wei, Link-Pérez, Melanie, Liu, Hong-Mei, Lu, Ngan Thi, Meza-Torres, Esteban I, Miao, Xin-Yuan, Moran, Robbin, Mynsson, Claudine Massi, Nagalingum, Nathalie, Øllgaard, Benjamin, Paul, Alison M, Pereira, Jovani B de S, Perrie, Leon R, Ponce, Mónica, Ranker, Tom A, Schulz, Christian, Shinohara, Wataru, Shmakov, Alexander, Sigel, Erin M, de Souza, Filipe Soares, Sylvestre, Lana da Silva, Testo, Weston, Triana-Moreno, Luz Amparo, Tsutsumi, Chie, Tuomisto, Hanna, Valdespino, Iván A, Vasco, Alejandra, Viveros, Raquel Stauffer, Weakley, Alan, Wei, Ran, Weststrand, Stina, Wolf, Paul G, Yatskievych, George, Xu, Xiao-Gang, Yan, Yue-Hong, Zhang, Liang, Zhang, Xian-Chun, Zhou, Xin-Mao, Pteridophyte Phylogeny Group, The, Schuettpelz, Eric, Schneider, Harald, Smith, Alan R, Hovenkamp, Peter, Prado, Jefferson, Rouhan, Germinal, Salino, Alexandre, Sundue, Michael, Almeida, Thaís Elias, Parris, Barbara, Sessa, Emily B, FIeld, Ashley R, de Gasper, André Luís, Rothfels, Carl J, Windham, Michael D, Lehnert, Marcus, Dauphin, Benjamin, Ebihara, Atsushi, Lehtonen, Samuli, Schwartsburd, Pedro Bond, Metzgar, Jordan, Zhang, L-Bing, Kuo, Li-Yaung, Brownsey, Patrick J, Kato, Masahiro, Arana, Marcelo Daniel, Assis, Francince C, Barker, Michael S, Barrington, David S, Chang, Ho-Ming, Chang, Yi-Han, Chao, Yi-Shan, Chen, Cheng-Wei, Chen, De-Kui, Chiou, Wen-Liang, Dittrich, Jose María Gabriel, Duan, Yi-Fan, Dubuisson, Jean-Yves, Farrar, Donald R, Fawcett, Susan, Galán, Jose María Gabriel y, Góes-Neto, Luiz Armando de Araújo, Grant, Jason R, Grusz, Amanda L, Haufler, Christopher, Hauk, Warren, He, Hai, Hennequin, Sabine, Hirai, Regina Yoshie, Huiet, Layne, Kessler, Michael, Korall, Petra, Labiak, Paulo H, Larsson, Anders, León, Blanca, Li, Chun-Xiang, Li, Fay-Wei, Link-Pérez, Melanie, Liu, Hong-Mei, Lu, Ngan Thi, Meza-Torres, Esteban I, Miao, Xin-Yuan, Moran, Robbin, Mynsson, Claudine Massi, Nagalingum, Nathalie, Øllgaard, Benjamin, Paul, Alison M, Pereira, Jovani B de S, Perrie, Leon R, Ponce, Mónica, Ranker, Tom A, Schulz, Christian, Shinohara, Wataru, Shmakov, Alexander, Sigel, Erin M, de Souza, Filipe Soares, Sylvestre, Lana da Silva, Testo, Weston, Triana-Moreno, Luz Amparo, Tsutsumi, Chie, Tuomisto, Hanna, Valdespino, Iván A, Vasco, Alejandra, Viveros, Raquel Stauffer, Weakley, Alan, Wei, Ran, Weststrand, Stina, Wolf, Paul G, Yatskievych, George, Xu, Xiao-Gang, Yan, Yue-Hong, Zhang, Liang, Zhang, Xian-Chun, and Zhou, Xin-Mao

Published
2017

87. A Revision of Neotropical Bonyunia (Loganiaceae: Antonieae)

Author

Grant, Jason R and Grant, Jason R

Abstract

A revision of the Neotropical genus Bonyunia M. R. Schomb. ex Progel (Loganiaceae, Antonieae) is provided, including a key to species, description, distribution, IUCN Red List status, and discussion. Bonyunia is morphologically and ecologically diverse with taxonomically informative characters that include habit, seed and leaf morphology, and the shape and indument of the calyx, bracts, and bracteoles. Bonyunia occurs in lowland regions of the Amazon River watershed (Brazil and Bolivia), the Orinoco River watershed (Colombia and Venezuela), tepuis of the Guayana region and outliers (Brazil, Guyana, Venezuela, and Colombia), and lowland regions of Amazon Basin–facing Andes in Peru, throughout on white sands. Ten species are recognized, including four established species: B. antoniifolia Progel, B. aquatica Ducke, B. minor N. E. Br. (including B. cinchonoides Gleason & Standl.), and B. superba M. R. Schomb. ex Progel. Six species are newly described: B. excelsa J. R. Grant (Colombia), B. magnifica J. R. Grant (Brazil), B. nobilis J. R. Grant (Colombia), B. pulchra Ricketson, J. R. Grant & Liesner (Peru), B. spectabilis J. R. Grant (Guyana), and B. venusta J. R. Grant (Brazil).

Published
2017

88. Convergent Vessel Diameter–Stem Diameter Scaling across Five Clades of New and Old World Eudicots from Desert to Rain Forest

Author

Olson, Mark E, Rosell, Julieta A, León, Calixto, Zamora, Salvador, Weeks, Andrea, Alvarado-Cardenas, Leonardo O, Ivalu Cacho, N, Grant, Jason R, Olson, Mark E, Rosell, Julieta A, León, Calixto, Zamora, Salvador, Weeks, Andrea, Alvarado-Cardenas, Leonardo O, Ivalu Cacho, N, and Grant, Jason R

Abstract

Premise of research. Variation in average xylem vessel diameter across species has important functional consequences, but the causes of this variation remain unclear. Average vessel diameter is known to scale with stem size within and across species. Vessel diameter also seems to differ between clades and across environments, with dryland plants having narrower, more cavitation-resistant vessels. As a result, it is not clear to what extent phylogenetic affinity and environment are associated with differences in the vessel diameter–stem size relationship. Methodology. With linear models and correlations, we explored the influence of environment and phy- logeny on the vessel diameter–stem diameter relationship in a molecular phylogenetic context across 83 species in four families spanning desert to rain forest in the Americas, Africa, Asia, and Madagascar. Pivotal results. Mean species vessel diameter was strongly predicted by trunk diameter (slope ∼ 0.33), and this slope was not affected by either phylogenetic affinity or environment. Clades differed only slightly in mean vessel diameter when controlling for stem size, and there was no tendency for plants of moist environments to have wider vessels. Of four climate indexes, only the temperature index contributed to explaining vessel diameter, although very weakly. Conclusions. Our results are congruent with models suggesting that natural selection should maximize vessel conductivity while minimizing cavitation risk via vessel taper in the context of conductive path length. Because neither environment nor phylogeny contributed to explaining vessel diameter–stem diameter scaling across species, our results appear congruent with the notion that selection favoring cavitation resistance via narrow vessels should lead to shorter statures independently of ancestry or habitat. The repeated finding of narrow vessels in dryland plants might therefore reflect the smaller average stem s

Published
2017

89. Wood anatomy of Gentianaceae, tribe Helieae, in relation to ecology, habit, systematics, and sample diameter

Author

Carlquist, Sherwin, Grant, Jason R, Carlquist, Sherwin, and Grant, Jason R

Abstract

Twenty collections representing one species each of Symbolanthus and Tachia, and 17 species of Macrocarpaea were studied by means of light microscopy and scanning electron microscopy (SEM). Wood details show that the three genera form a coherent group; Tachia differs from the others in only a few minor characters. Because the species studied form a natural group, wood variations within Helieae offer the basis for correlations and interpretations with respect to habit and ecology. Diameter of stems studied proves to be an important variable that must be taken into account. Correlations with stem diameter include wider vessels in outer wood of wider samples. This would correspond to deeper penetration of reliable water tables by roots of helioid trees or large shrubs. Ray height decreases with increase in stem diameter, an indication of paedomorphosis. Rays of all species are paedomorphic in histology by virtue of relative paucity or even absence of procumbent cells in multiseriate rays. Pseusoscalariform lateral wall pitting of vessels is also a feature characteristic of paedomorphosis. The assemblage of paedomorphic features correlates well with the conclusion, reached by authors who used cladistic methods, that Gentianaceae other than Gentianeae are derived from suffrutescent prennials. The Mesomorphy Ratio, which incorporates three vessel features, correlates with leaf length and with stem diameter. All Helieae are mesophytic, but to various degrees. Septate fiber-tracheids, where present, are typically near vessels and form a substitute for or an addendum to vasicentric axial parenchyma as a mechanism for photosynthate storage. Vestured pits occur on lateral wall pits of vessels of all Helieae, but not on the fibertracheids. Vestured pits show diversity within Macrocarpaea, a feature of possible systematic significance.

Published
2017

90. Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Author

German, Dmitry A, Grant, Jason R, Lysak, Martin A, Al-Shehbaz, Ihsan A, German, Dmitry A, Grant, Jason R, Lysak, Martin A, and Al-Shehbaz, Ihsan A

Abstract

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification. KeywordsBrassicaceae–Chorisporeae–Generic delimitation–Phylogeny–Parrya.

Published
2017

91. New combinations and names in Andean Pitcairnia, Tillandsia, and Werauhia

Author

Grant, Jason R and Grant, Jason R

Abstract

The following eight new combinations are made based on transfers from Pepinia and Vriesea: Pitcairnia holstii (H. Luther) J. R. Grant, P. minicorallina (H. Luther) J. R. Grant, P. neeana (L. B. Sm. ex H. Luther) J. R. Grant, P. peruana (H. Luther) J. R. Grant, Tillandsia appenii (Rauh) J. R. Grant, T. gruberi (Ehlers) J. R. Grant, T. lutheri (Manzan. & W. Till) J. R. Grant, and T. piepenbringii (Rauh) J. R. Grant. Additionally, three new names are proposed: Tillandsia frank-hasei J. R. Grant to replace Vriesea hasei Ehlers, T. walter-tillii J. R. Grant to replace V. tillii Manzan., and Werauhia rauhii J. R. Grant to replace V. patzeltii Rauh var. panamaensis Rauh at the species rank., O autor propõe oito novas combinações baseadas na transferência de espécies dos gêneros Pepinia e Vriesea, a saber: Pitcairnia holstii (H. Luther) J. R.Grant, P. minicorallina (H. Luther) J. R. Grant, P. neeana (L. B. Sm. ex H. Luther) J. R. Grant, P. peruana (H. Luther) J. R. Grant, Tillandsia appenii (Rauh) J. R. Grant, T. gruberi (Ehlers) J. R. Grant, T. lutheri (Manzan. & W. Till) J. R. Grant, e T. piepenbringii (Rauh) J. R. Grant. Além disso, são propostos três novos nomes: Tillandsia frankhasei J. R. Grant, em substituição a Vriesea hasei Ehlers, T. walter-tillii J. R. Grant para substituir V. tillii Manzan. e Werauhia rauhii J. R. Grant para substituir, no status de espécie, V. patzeltii Rauh var. panamaensis Rauh.

Published
2017

92. DrugBank 5.0: a major update to the DrugBank database for 2018

Author

Wishart, David S, primary, Feunang, Yannick D, additional, Guo, An C, additional, Lo, Elvis J, additional, Marcu, Ana, additional, Grant, Jason R, additional, Sajed, Tanvir, additional, Johnson, Daniel, additional, Li, Carin, additional, Sayeeda, Zinat, additional, Assempour, Nazanin, additional, Iynkkaran, Ithayavani, additional, Liu, Yifeng, additional, Maciejewski, Adam, additional, Gale, Nicola, additional, Wilson, Alex, additional, Chin, Lucy, additional, Cummings, Ryan, additional, Le, Diana, additional, Pon, Allison, additional, Knox, Craig, additional, and Wilson, Michael, additional

Published
2017
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94. Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection

Author

Kommadath, Arun, primary, Bao, Hua, additional, Choi, Igseo, additional, Reecy, James M., additional, Koltes, James E., additional, Fritz-Waters, Elyn, additional, Eisley, Chris J., additional, Grant, Jason R., additional, Rowland, Robert R. R., additional, Tuggle, Christopher K., additional, Dekkers, Jack C. M., additional, Lunney, Joan K., additional, Guan, Le Luo, additional, Stothard, Paul, additional, and Plastow, Graham S., additional

Published
2017
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95. Tradescantia boliviana (Commelinaceae), a New Combination for an Overlooked South American Species

Author

Grant, Jason R

Abstract

The new combination Tradescantia boliviana (Hasskarl) J. R. Grant is made in recognition that it is a distinct species widespread in Peru, Bolivia, Paraguay, and Argentina, here separatedby morphological characters and distribution from its previous inclusion within T. ambigua Martius ex J. H. Schultes, which is restricted to northeastern Brazil.

Published
2015

98. DE MACROCARPAEAE GRISEBACH (EX GENTIANACEIS) SPECIEBUS NOVIS VIII: FOUR NEW SPECIES FROM ECUADOR

Author

Grant, Jason R

Abstract

Two new species, Macrocarpaea claireae and M. quizhpei (Gentianaceae: Helieae), are described from the Huancabamba region of southern Ecuador. Macrocarpaea claireae occurs around Valladolid, adjacent to P. N. Podocarpus, and M. quizhpei occurs in the Nangaritza watershed. M. claireae is closely related to M. pringleana and M. sodiroana, yet differs notably in its glaucous-green, campanulate-urceolate calyx. Macrocarpaea quizhpei has affinities to M. dies-viridis, but differs in having a large, diffusely branched, open thyrse to 1.3 m high.

Published
2015

100. DE MACROCARPAEAE GRISEBACH (EX GENTIANACEIS) SPECIEBUS NOVIS VI: SEED MORPHOLOGY, PALYNOLOGY, AN INFRAGENERIC CLASSIFICATION , AND ANOTHER TWENTY-THREE NEW SPECIES LARGELY FROM COLOMBIA

Author

Grant, Jason R

Abstract

A brief survey of seed morphology and palynology in Macrocarpaea is discussed and illustrated by Scanning Electron Microscopy (SEM) photographs. An infrageneric classification is presented where four sections are recognized: sect. Tabacifoliae, sect. Macrocarpaea, sect. Magnolifoliae, and sect. Choriophylla. Another 23 new species, largely from Colombia, are here described and illustrated: Brazil (1): M. illecebrosa; Colombia (14): M. betancuriana, M. callejasii, M. gaudialis, M. gondoloides, M. gravabilis, M. gulosa, M. hilarula, M. jocularis, M. lacrossiformis, M. laudabilis, M. maryae, M. silverstonei, M. umerulus, and M. ypsilocaule; Ecuador (4): M. berryi, M. jactans, M. neillii, and M. voluptuosa; and Peru (4): M. chthonotropa, M. granpajatena, M. quechua, and M. xerantifulva.

Published
2015

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