Genome sequence of the palaeopolyploid soybean
Jeremy Schmutz,Steven B. Cannon,Jessica A. Schlueter,Jessica A. Schlueter,Jianxin Ma,Therese Mitros,William Nelson,David L. Hyten,Qijian Song,Qijian Song,Jay J. Thelen,Jianlin Cheng,Dong Xu,Uffe Hellsten,Gregory D. May,Yeisoo Yu,Tetsuya Sakurai,Taishi Umezawa,Madan K. Bhattacharyya,Devinder Sandhu,Babu Valliyodan,Erika Lindquist,Myron Peto,David Grant,Shengqiang Shu,David Goodstein,Kerrie Barry,Montona Futrell-Griggs,Brian Abernathy,Jianchang Du,Zhixi Tian,Liucun Zhu,Navdeep Gill,Trupti Joshi,Marc Libault,Ananad Sethuraman,Xue-Cheng Zhang,Kazuo Shinozaki,Henry T. Nguyen,Rod A. Wing,Perry B. Cregan,James E. Specht,Jane Grimwood,Daniel S. Rokhsar,Gary Stacey,Randy C. Shoemaker,Scott A. Jackson +46 more
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TLDR
An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.Abstract:
Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.read more
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High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane.
Olivier Garsmeur,Carine Charron,Stéphanie Bocs,Vincent Jouffe,Sylvie Samain,Arnaud Couloux,Gaëtan Droc,Cyrille Zini,Jean-Christophe Glaszmann,Marie-Anne Van Sluys,Angélique D'Hont +10 more
TL;DR: In this article, the authors compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones) to investigate the genome dynamics in this highly polyploid context, and revealed a high level of gene retention and colinearity.
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Update on Chloroplast Research: New Tools, New Topics, and New Trends
TL;DR: The knowledge of many chloroplast processes, notably photosynthesis and photorespiration, has reached such an advanced state that biotechnological approaches to crop improvement now seem feasible.
Journal ArticleDOI
Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean Functional Genomics
Yaya Cui,Shyam Barampuram,Minviluz G. Stacey,C. Nathan Hancock,Seth D. Findley,Melanie Mathieu,Zhanyuan J. Zhang,Wayne A. Parrott,Gary Stacey +8 more
TL;DR: The data demonstrate the Tnt1 retrotransposon to be a powerful system that can be used for effective large-scale insertional mutagenesis in soybean.
Journal ArticleDOI
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Amit Rai,Hideki Hirakawa,Ryo Nakabayashi,Shinji Kikuchi,Koki Hayashi,Megha Rai,Hiroshi Tsugawa,Taiki Nakaya,Tetsuya Mori,Hideki Nagasaki,Runa Fukushi,Yoko Kusuya,Hiroki Takahashi,Hiroshi Uchiyama,Atsushi Toyoda,Shoko Hikosaka,Eiji Goto,Kazuki Saito,Mami Yamazaki +18 more
TL;DR: Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, a working model for MIA evolution, and a pangenome for MIA biosynthesis are proposed, which will help in establishing a sustainable supply of camptothecin.
Journal ArticleDOI
Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana
TL;DR: The evolutionary importance of reciprocal expression patterns between gene duplicates is indicated, showing that they are common, often associated with regulatory neofunctionalization, and may be a factor allowing for retention and divergence of duplicated genes.
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