Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Daniel Koenig,José M. Jiménez-Gómez,Seisuke Kimura,Daniel Fulop,Daniel H. Chitwood,Lauren R. Headland,Ravi Kumar,Michael F. Covington,Upendra K. Devisetty,An V. Tat,Takayuki Tohge,Anthony Bolger,Korbinian Schneeberger,Stephan Ossowski,Christa Lanz,Guangyan Xiong,Mallorie Taylor-Teeples,Siobhan M. Brady,Markus Pauly,Detlef Weigel,Björn Usadel,Alisdair R. Fernie,Jie Peng,Neelima Sinha,Julin N. Maloof +24 more
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TLDR
High-throughput sequencing is used to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives and identifies hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives.Abstract:
Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.read more
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The genome of the stress-tolerant wild tomato species Solanum pennellii
Anthony Bolger,Federico Scossa,Marie E. Bolger,Christa Lanz,Florian Maumus,Takayuki Tohge,Hadi Quesneville,Saleh Alseekh,Iben Sørensen,Gabriel Lichtenstein,Eric A. Fich,Mariana Conte,Heike Keller,Korbinian Schneeberger,Rainer Schwacke,Itai Ofner,Julia Vrebalov,Yimin Xu,Sonia Osorio,Saulo Alves Aflitos,Elio Schijlen,José M. Jiménez-Gómez,Małgorzata Ryngajłło,Seisuke Kimura,Ravi Kumar,Daniel Koenig,Lauren R. Headland,Julin N. Maloof,Neelima Sinha,Roeland C. H. J. van Ham,René Klein Lankhorst,Linyong Mao,Alexander Vogel,Borjana Arsova,Ralph Panstruga,Zhangjun Fei,Jocelyn K. C. Rose,Dani Zamir,Fernando Carrari,James J. Giovannoni,Detlef Weigel,Björn Usadel,Alisdair R. Fernie +42 more
TL;DR: A high-quality genome assembly of the parents of the IL population of S. pennellii is described, defining candidate genes for stress tolerance and providing evidence that transposable elements had a role in the evolution of these traits.
Journal ArticleDOI
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing
Saulo Alves Aflitos,Elio Schijlen,Hans de Jong,Dick de Ridder,Sandra Smit,Richard Finkers,Jun Wang,Gengyun Zhang,Ning Li,Likai Mao,Freek T. Bakker,Rob Dirks,Timo M. Breit,Barbara Gravendeel,Henk Huits,Darush Struss,Ruth A. Swanson-Wagner,Hans C. van Leeuwen,Roeland C. H. J. van Ham,Laia Fito,Laëtitia Guignier,Myrna Sevilla,Philippe Ellul,Eric W. Ganko,Arvind Kapur,Emannuel Reclus,Bernard de Geus,Henri van de Geest,Bas te Lintel Hekkert,Jan C. van Haarst,Lars Smits,Andries Koops,Gabino F. Sanchez-Perez,Adriaan W. van Heusden,Richard G. F. Visser,Zhiwu Quan,Jiumeng Min,Li Liao,Xiaoli Wang,Guangbiao Wang,Zhen Yue,Xinhua Yang,Na Xu,Eric Schranz,Erik Smets,Rutger A. Vos,Johan Rauwerda,Remco Ursem,Cees Schuit,Mike Kerns,Jan van den Berg,Wim H. Vriezen,Antoine Janssen,Erwin Datema,Torben Jahrman,Frederic Moquet,Julien Bonnet,Sander Peters +57 more
TL;DR: Results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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
Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model
Mily Ron,Kaisa Kajala,Germain Pauluzzi,Dongxue Wang,Mauricio Reynoso,Kristina Zumstein,Jasmine Garcha,Sonja Winte,Helen Masson,Soichi Inagaki,Fernán Federici,Neelima Sinha,Roger B. Deal,Julia Bailey-Serres,Siobhan M. Brady +14 more
TL;DR: Testing tomato gene expression with tagged nuclei and ribosomes and CRISPR/Cas9 genome editing shows conservation of SHORT-ROOT gene function, and transcriptional reporters, translational reporters, and clustered regularly interspaced short palindromic repeats-associated nuclease9 genome edited demonstrate that SH short-roOT and SCARECROW gene function is conserved between Arabidopsis (Arabidopsis thaliana) and tomato.
Journal ArticleDOI
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Mikkel Schubert,Hakon Jonsson,Dan Chang,Clio Der Sarkissian,Luca Ermini,Aurélien Ginolhac,Anders Albrechtsen,Isabelle Dupanloup,Isabelle Dupanloup,Adrien Foucal,Adrien Foucal,Bent O. Petersen,Matteo Fumagalli,Maanasa Raghavan,Andaine Seguin-Orlando,Thorfinn Sand Korneliussen,Amhed Missael Vargas Velazquez,Jesper Stenderup,Cindi A. Hoover,Carl-Johan Rubin,Ahmed H. Alfarhan,Saleh A. Alquraishi,Khaled A. S. Al-Rasheid,David E. MacHugh,Ted Kalbfleisch,James N. MacLeod,Edward M. Rubin,Thomas Sicheritz-Pontén,Leif Andersson,Michael Hofreiter,Tomas Marques-Bonet,M. Thomas P. Gilbert,Rasmus Nielsen,Laurent Excoffier,Laurent Excoffier,Eske Willerslev,Beth Shapiro,Ludovic Orlando +37 more
TL;DR: In this article, the authors sequenced two ancient horse genomes from Taymyr, Russia (at 7.4 and 24.3fold coverage) and compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene.
References
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