Journal ArticleDOI
Genome-wide investigation on the genetic variations of rice disease resistance genes
Sihai Yang,Zhumei Feng,Xiuyan Zhang,Ke Jiang,Xinqing Jin,Yue-Yu Hang,Jian-Qun Chen,Dacheng Tian +7 more
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TLDR
A genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes is reported, indicating that the observed variation pattern may be common in all rice lines.Abstract:
Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93-11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable "artificially selective sweeping" could be detected in a large proportion of the conserved R-genes, a scenario described in the "arms race" co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.read more
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Recent duplications dominate NBS-encoding gene expansion in two woody species.
TL;DR: It is suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species, and could compensate for the longer generation time in woody perennial species e.g. duplication and recombination.
Journal ArticleDOI
Functional Annotation, Genome Organization and Phylogeny of the Grapevine ( Vitis vinifera ) Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays
Diane M. Martin,Sébastien Aubourg,Marina B Schouwey,Laurent Daviet,Michel Schalk,Omid Toub,Steven T. Lund,Joerg Bohlmann +7 more
TL;DR: The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine and is provided with detailed experimental functional annotation of 39 members of this important gene family in Grapevine and comprehensive information about gene structure and phylogeny.
Journal ArticleDOI
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Joshua C. Stein,Yeisoo Yu,Dario Copetti,Dario Copetti,Derrick J. Zwickl,Li Zhang,Chengjun Zhang,Kapeel Chougule,Kapeel Chougule,Dongying Gao,Aiko Iwata,Jose Luis Goicoechea,Sharon Wei,Jun Wang,Yi Liao,Muhua Wang,Muhua Wang,Julie Jacquemin,Julie Jacquemin,Claude Becker,Dave Kudrna,Jianwei Zhang,Carlos E.M. Londono,Xiang Song,Seunghee Lee,Paul L. Sanchez,Paul L. Sanchez,Andrea Zuccolo,Andrea Zuccolo,Jetty S.S. Ammiraju,Jetty S.S. Ammiraju,Jayson Talag,Ann Danowitz,Luis F. Rivera,Andrea R. Gschwend,Christos Noutsos,Cheng chieh Wu,Cheng chieh Wu,Shu-Min Kao,Shu-Min Kao,Jhih wun Zeng,Fu Jin Wei,Qiang Zhao,Qi Feng,Moaine El Baidouri,Marie-Christine Carpentier,Eric Lasserre,Richard Cooke,Daniel da Rosa Farias,Luciano Carlos da Maia,Railson Schreinert dos Santos,Kevin G. Nyberg,Kenneth L. McNally,Ramil Mauleon,Nickolai Alexandrov,Jeremy Schmutz,Dave Flowers,Chuanzhu Fan,Detlef Weigel,Kshirod K. Jena,Thomas Wicker,Mingsheng Chen,Bin Han,Robert J Henry,Yue-Ie C. Hsing,Nori Kurata,Antonio Costa de Oliveira,Olivier Panaud,Scott A. Jackson,Carlos A. Machado,Michael J. Sanderson,Manyuan Long,Doreen Ware,Doreen Ware,Rod A. Wing,Rod A. Wing +75 more
TL;DR: This study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species and announcing many new haplotypes of potential use for future crop protection.
Journal ArticleDOI
Plant Nucleotide Binding Site–Leucine-Rich Repeat (NBS-LRR) Genes: Active Guardians in Host Defense Responses
TL;DR: Recent findings have provided insights into the roles of alternative splicing, the ubiquitin/proteasome system, and miRNAs and secondary siRNAs in the regulation of NBS-LRR gene expression at the post-transcriptional, post- translational and epigenetic levels.
Journal ArticleDOI
Identification and localisation of the NB-LRR gene family within the potato genome
Florian Jupe,Florian Jupe,Leighton Pritchard,Graham J Etherington,Katrin MacKenzie,Peter J. A. Cock,Frank Wright,Sanjeev Kumar Sharma,Dan Bolser,Glenn J. Bryan,Jonathan D. G. Jones,Ingo Hein +11 more
TL;DR: By establishing the phylogenetic and positional relationship of potato NB-LRRs, the analysis offers significant insight into the evolution of potato R genes and provides a blueprint for future efforts to identify and more rapidly clone functional NB- LRR genes from Solanum species.
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