A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species.
Daniel C. Ilut,Jeremy E. Coate,Amelia K. Luciano,Thomas G. Owens,Gregory D. May,Andrew Farmer,Jeff J. Doyle +6 more
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TLDR
A novel metric developed to address issues arising from high degrees of gene space duplication and a method for dissecting a gene's measured transcript level in a polyploid species into the relative contribution of its homoeologues are presented.Abstract:
Premise of the study: RNA-seq analysis of plant transcriptomes poses unique challenges due to the highly duplicated nature of plant genomes. We address these challenges in the context of recently formed polyploid species and detail an RNA-seq experiment comparing the leaf transcriptome profi le of an allopolyploid relative of soybean with the diploid species that contributed its homoeologous genomes. Methods: RNA-seq reads were obtained from the three species and were aligned against the genome sequence of Glycine max. Transcript levels were estimated for each gene, relative contributions of polyploidy-duplicated loci (homoeologues) in the tetraploid were identifi ed, and comparisons of transcript profi les and individual genes were used to analyze the regulation of transcript levels. Key results: We present a novel metric developed to address issues arising from high degrees of gene space duplication and a method for dissecting a gene ’ s measured transcript level in a polyploid species into the relative contribution of its homoeologues. We identify the gene family likely contributing to differences in photosynthetic rate between the allotetraploid and its progenitors and show that the tetraploid appears to be using the “ redundant ” gene copies in novel ways. Conclusions: Given the prevalence of polyploidy events in plants, we believe many of the approaches developed here to be applicable, and often necessary, in most plant RNA-seq experiments. The deep sampling provided by RNA-seq allows us to dissect the genetic underpinnings of specifi c phenotypes as well as examine complex interactions within polyploid genomes.read more
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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Boulos Chalhoub,Shengyi Liu,Isobel A. P. Parkin,Haibao Tang,Haibao Tang,Xiyin Wang,Julien Chiquet,Harry Belcram,Chaobo Tong,Birgit Samans,Margot Correa,Corinne Da Silva,Jérémy Just,Cyril Falentin,Chu Shin Koh,Isabelle Le Clainche,Maria Bernard,Pascal Bento,Benjamin Noel,Karine Labadie,Adriana Alberti,Mathieu Charles,Dominique Arnaud,Hui Guo,Christian Daviaud,Salman Alamery,Kamel Jabbari,Kamel Jabbari,Meixia Zhao,Patrick P. Edger,Houda Chelaifa,David C. Tack,Gilles Lassalle,Imen Mestiri,Nicolas Schnel,Marie-Christine Le Paslier,Guangyi Fan,Victor Renault,Philippe E. Bayer,Agnieszka A. Golicz,Sahana Manoli,Tae-Ho Lee,Vinh Ha Dinh Thi,Smahane Chalabi,Qiong Hu,Chuchuan Fan,Reece Tollenaere,Yunhai Lu,Christophe Battail,Jinxiong Shen,Christine Sidebottom,Xinfa Wang,Aurélie Canaguier,Aurélie Chauveau,Aurélie Bérard,G. Deniot,Mei Guan,Zhongsong Liu,Fengming Sun,Yong Pyo Lim,Eric Lyons,Christopher D. Town,Ian Bancroft,Xiaowu Wang,Jinling Meng,Jianxin Ma,J. Chris Pires,Graham J.W. King,Dominique Brunel,Régine Delourme,Michel Renard,Jean-Marc Aury,Keith L. Adams,Jacqueline Batley,Jacqueline Batley,Rod J. Snowdon,Jörg Tost,David Edwards,David Edwards,Yongming Zhou,Wei Hua,Andrew G. Sharpe,Andrew H. Paterson,Chunyun Guan,Patrick Wincker,Patrick Wincker,Patrick Wincker +86 more
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Journal ArticleDOI
Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades
Anne Bruneau,Jeff J. Doyle,Patrick S. Herendeen,Colin E. Hughes,Gregory Kenicer,Gwilym P. Lewis,Barbara A. Mackinder,R.T. Pennington,Michael J. Sanderson,Martin F. Wojciechowski,S. Boatwright,Gillian K. Brown,Domingos Cardoso,M. Crips,Ashley N. Egan,R. Fortunato,Julie A. Hawkins,T. Kajita,Bente B. Klitgaard,Erik J. M. Koenen,Matt Lavin,M. Luckow,Brigitte Marazzi,Michelle M. McMahon,Joseph T. Miller,Daniel J. Murphy,H. Ohashi,L. P. de Queiroz,L. Rico,Tiina Särkinen,B. Schrire,Marcelo F. Simon,Edivan Rodrigues de Souza,Kelly P. Steele,B.M. Torke,Jan J. Wieringa,B.E. Wijk +36 more
TL;DR: This work examines how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the Leguminosae, and examines how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification.
Journal ArticleDOI
Genomics of crop wild relatives: expanding the gene pool for crop improvement
TL;DR: Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks.
Journal ArticleDOI
Applications of next-generation sequencing in plant biology.
TL;DR: This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.
Journal ArticleDOI
Polyploidy: Pitfalls and paths to a paradigm.
Douglas E. Soltis,Douglas E. Soltis,Clayton J. Visger,Clayton J. Visger,D. Blaine Marchant,D. Blaine Marchant,Pamela S. Soltis,Pamela S. Soltis +7 more
TL;DR: While certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se, it is found that the path to synthesis is hindered by numerous gaps in knowledge of even the best-known systems.
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