PlnTFDB: updated content and new features of the plant transcription factor database
Paulino Pérez-Rodríguez,Diego Mauricio Riaño-Pachón,Luiz Gustavo Guedes Corrêa,Stefan A. Rensing,Birgit Kersten,Bernd Mueller-Roeber +5 more
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TLDR
The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors and other transcriptional regulators in plant species whose genomes have been completely sequenced and annotated.Abstract:
The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.read more
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PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.
TL;DR: With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, the upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/).
Journal ArticleDOI
A reference genome for common bean and genome-wide analysis of dual domestications
Jeremy Schmutz,Phillip E. McClean,Sujan Mamidi,G Albert Wu,Steven B. Cannon,Jane Grimwood,Jerry Jenkins,Shengqiang Shu,Qijian Song,Carolina Chavarro,Mirayda Torres-Torres,Valérie Geffroy,Samira Mafi Moghaddam,Dongying Gao,Brian Abernathy,Kerrie Barry,Matthew W. Blair,Mark A. Brick,Mansi Chovatia,Paul Gepts,David Goodstein,Michael D. Gonzales,Uffe Hellsten,David L. Hyten,Gaofeng Jia,James D. Kelly,Dave Kudrna,Rian Lee,Manon M.S. Richard,Phillip N. Miklas,Juan M. Osorno,Josiane Rodrigues,Vincent Thareau,Carlos A. Urrea,Mei Wang,Yeisoo Yu,Ming Zhang,Rod A. Wing,Perry B. Cregan,Daniel S. Rokhsar,Scott A. Jackson +40 more
TL;DR: 2 independent domestications from genetic pools that diverged before human colonization are confirmed and a set of genes linked with increased leaf and seed size are identified and combined with quantitative trait locus data from Mesoamerican cultivars.
Journal ArticleDOI
NAC proteins: regulation and role in stress tolerance
TL;DR: This review summarizes the recent progress in research on NACs highlighting the proteins' potential for engineering stress tolerance against various abiotic and biotic challenges and their prospective role for crop improvement strategies via biotechnological intervention.
Journal ArticleDOI
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
Seungill Kim,Minkyu Park,Seon-In Yeom,Yong-Min Kim,Je Min Lee,Hyun-Ah Lee,Eunyoung Seo,Jaeyoung Choi,Kyeongchae Cheong,Ki-Tae Kim,Kyongyong Jung,Gir-Won Lee,Sang-Keun Oh,Chungyun Bae,Saet-Byul Kim,Hyeyoung Lee,Shin Young Kim,Myung-Shin Kim,Byoung-Cheorl Kang,Yeong Deuk Jo,Hee Bum Yang,Hee-Jin Jeong,Won-Hee Kang,Jin Kyung Kwon,Chanseok Shin,Jae Yun Lim,June Hyun Park,Jin Hoe Huh,June Sik Kim,Byung-Dong Kim,Oded Cohen,Ilan Paran,Mi Chung Suh,Saet Buyl Lee,Yeon Ki Kim,Younhee Shin,Seung-Jae Noh,Junhyung Park,Young Sam Seo,Suk-Yoon Kwon,Hyun A Kim,Jeong Mee Park,Hyunjin Kim,Sang Bong Choi,Paul W. Bosland,Gregory Reeves,Sung Hwan Jo,Bong Woo Lee,Hyung-Taeg Cho,Hee-Seung Choi,Min-Soo Lee,Yeisoo Yu,Yang Do Choi,Beom Seok Park,Allen Van Deynze,Hamid Ashrafi,Theresa Hill,Woo Taek Kim,Hyun Sook Pai,Hee-Kyung Ahn,Inhwa Yeam,James J. Giovannoni,James J. Giovannoni,Jocelyn K. C. Rose,Iben Sørensen,Sang Jik Lee,Ryan W. Kim,Ik-Young Choi,Beom-Soon Choi,Jong-Sung Lim,Yong-Hwan Lee,Doil Choi +71 more
TL;DR: The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements.
Journal ArticleDOI
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
TL;DR: The plant TF database PlantTFDB is updated to version 3.0, with more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs.
References
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Journal ArticleDOI
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
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TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Journal ArticleDOI
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Olivier Jaillon,Jean-Marc Aury,Benjamin Noel,Alberto Policriti,Christian Clepet,Alberto Casagrande,Nathalie Choisne,Sébastien Aubourg,Nicola Vitulo,Claire Jubin,Alessandro Vezzi,Fabrice Legeai,Philippe Hugueney,Corinne Dasilva,David S. Horner,Erica Mica,Delphine Jublot,Julie Poulain,Clémence Bruyère,Alain Billault,Béatrice Segurens,Michel Gouyvenoux,Edgardo Ugarte,Federica Cattonaro,Véronique Anthouard,Virginie Vico,Cristian Del Fabbro,Michael Alaux,Gabriele Di Gaspero,Vincent Dumas,Nicoletta Felice,Sophie Paillard,Irena Juman,Marco Moroldo,Simone Scalabrin,Aurélie Canaguier,Isabelle Le Clainche,G Malacrida,Eléonore Durand,Graziano Pesole,Valérie Laucou,Philippe Chatelet,Didier Merdinoglu,Massimo Delledonne,Mario Pezzotti,Alain Lecharny,Claude Scarpelli,François Artiguenave,M. Enrico Pè,Giorgio Valle,Michele Morgante,Michel Caboche,Anne-Françoise Adam-Blondon,Jean Weissenbach,Francis Quetier,Patrick Wincker +55 more
TL;DR: A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Journal ArticleDOI
The Sorghum bicolor genome and the diversification of grasses
Andrew H. Paterson,John E. Bowers,Rémy Bruggmann,Inna Dubchak,Jane Grimwood,Heidrun Gundlach,Georg Haberer,Uffe Hellsten,Therese Mitros,Alexander Poliakov,Jeremy Schmutz,Manuel Spannagl,Haibao Tang,Xiyin Wang,Xiyin Wang,Thomas Wicker,Arvind K. Bharti,Jarrod Chapman,F. Alex Feltus,F. Alex Feltus,Udo Gowik,Igor V. Grigoriev,Eric Lyons,Christopher G. Maher,Mihaela Martis,Apurva Narechania,Robert Otillar,Bryan W. Penning,Asaf Salamov,Yu Wang,Lifang Zhang,Nicholas C. Carpita,Michael Freeling,Alan R. Gingle,C. Thomas Hash,Beat Keller,Patricia E. Klein,Stephen Kresovich,Maureen C. McCann,Ray Ming,Daniel G. Peterson,Daniel G. Peterson,Mehboob-ur-Rahman,Mehboob-ur-Rahman,Doreen Ware,Doreen Ware,Peter Westhoff,Klaus F. X. Mayer,Joachim Messing,Daniel S. Rokhsar,Daniel S. Rokhsar +50 more
TL;DR: An initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome is presented, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information.
Journal ArticleDOI
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
Sabeeha S. Merchant,Simon E. Prochnik,Olivier Vallon,Elizabeth H. Harris,Steven J. Karpowicz,George B. Witman,Astrid Terry,Asaf Salamov,Lillian K. Fritz-Laylin,Laurence Maréchal-Drouard,Wallace F. Marshall,Liang-Hu Qu,David R. Nelson,Anton A. Sanderfoot,Martin H. Spalding,Vladimir V. Kapitonov,Qinghu Ren,Patrick J. Ferris,Erika Lindquist,Harris Shapiro,Susan Lucas,Jane Grimwood,Jeremy Schmutz,Pierre Cardol,Pierre Cardol,Heriberto Cerutti,Guillaume Chanfreau,Chun-Long Chen,Valérie Cognat,Martin T. Croft,Rachel M. Dent,Susan K. Dutcher,Emilio Fernández,Hideya Fukuzawa,David González-Ballester,Diego González-Halphen,Armin Hallmann,Marc Hanikenne,Michael Hippler,William Inwood,Kamel Jabbari,Ming Kalanon,Richard Kuras,Paul A. Lefebvre,Stéphane D. Lemaire,Alexey V. Lobanov,Martin Lohr,Andrea L Manuell,Iris Meier,Laurens Mets,Maria Mittag,Telsa M. Mittelmeier,James V. Moroney,Jeffrey L. Moseley,Carolyn A. Napoli,Aurora M. Nedelcu,Krishna K. Niyogi,Sergey V. Novoselov,Ian T. Paulsen,Greg Pazour,Saul Purton,Jean-Philippe Ral,Diego Mauricio Riaño-Pachón,Wayne R. Riekhof,Linda A. Rymarquis,Michael Schroda,David B. Stern,James G. Umen,Robert D. Willows,Nedra F. Wilson,Sara L. Zimmer,Jens Allmer,Janneke Balk,Katerina Bisova,Chong-Jian Chen,Marek Eliáš,Karla C Gendler,Charles R. Hauser,Mary Rose Lamb,Heidi K. Ledford,Joanne C. Long,Jun Minagawa,M. Dudley Page,Junmin Pan,Wirulda Pootakham,Sanja Roje,Annkatrin Rose,Eric Stahlberg,Aimee M. Terauchi,Pinfen Yang,Steven G. Ball,Chris Bowler,Carol L. Dieckmann,Vadim N. Gladyshev,Pamela J. Green,Richard A. Jorgensen,Stephen P. Mayfield,Bernd Mueller-Roeber,Sathish Rajamani,Richard T. Sayre,Peter Brokstein,Inna Dubchak,David Goodstein,Leila Hornick,Y. Wayne Huang,Jinal Jhaveri,Yigong Luo,Diego Martinez,Wing Chi Abby Ngau,Bobby Otillar,Alexander Poliakov,Aaron Porter,Lukasz Szajkowski,Gregory Werner,Kemin Zhou,Igor V. Grigoriev,Daniel S. Rokhsar,Daniel S. Rokhsar,Arthur R. Grossman +118 more
TL;DR: Analyses of the Chlamydomonas genome advance the understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
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