Dataset Information

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

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.

SUBMITTER: Koenig D

PROVIDER: S-EPMC3710864 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

Koenig Daniel D Jiménez-Gómez José M JM Kimura Seisuke S Fulop Daniel D Chitwood Daniel H DH Headland Lauren R LR Kumar Ravi R Covington Michael F MF Devisetty Upendra Kumar UK Tat An V AV Tohge Takayuki T Bolger Anthony A Schneeberger Korbinian K Ossowski Stephan S Lanz Christa C Xiong Guangyan G Taylor-Teeples Mallorie M Brady Siobhan M SM Pauly Markus M Weigel Detlef D Usadel Björn B Fernie Alisdair R AR Peng Jie J Sinha Neelima R NR Maloof Julin N JN

Proceedings of the National Academy of Sciences of the United States of America 20130626 28

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 pressur ...[more]

PMID: 23803858

Similar Datasets

Project description:Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the "all-ramie" transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation-reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering-promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.

Dataset Information

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

Publications

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets