RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat Triticum aestivum L.Report as inadecuate




RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat Triticum aestivum L. - Download this document for free, or read online. Document in PDF available to download.

Genome Biology

, 12:R119

First Online: 02 December 2011Received: 20 May 2011Revised: 25 August 2011Accepted: 02 December 2011

Abstract

BackgroundWhole genome duplication is a common evolutionary event in plants. Bread wheat Triticum aestivum L. is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes.

ResultsWe performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a set of 37,695 non-redundant sequence clusters, which is an unprecedented resolution corresponding to an estimated half of the wheat genome unigene repertoire. Using the Brachypodium distachyon genome as a reference for the Triticeae, we classified gene clusters into orthologous, paralogous, and homoeologous relationships. Based on this wheat gene evolutionary classification, older duplicated copies dating back 50 to 70 million years exhibit more than 80% gene loss and expression divergence while recent duplicates dating back 1.5 to 3 million years show only 54% gene loss and 36 to 49% expression divergence.

ConclusionsWe suggest that structural shuffling due to duplicated gene loss is a rapid process, whereas functional shuffling due to neo- and-or subfunctionalization of duplicates is a longer process, and that both shuffling mechanisms drive functional redundancy erosion. We conclude that, as a result of these mechanisms, half the gene duplicates in plants are structurally and functionally altered within 10 million years of evolution, and the diploidization process is completed after 45 to 50 million years following polyploidization.

AbbreviationsAFLPamplified fragment length polymorphism

bpbase pair

CALPcumulative alignment length percentage

CNVcopy number variation

CDScoding sequence

CIPcumulative identity percentage

COSconserved orthologous set

DDdegree day

ESTexpressed sequence tag

GOGene Ontology

HSPshigh scoring pairs

MYAmillion years ago

RFLPrestriction fragment length polymorphism

RNA-seqRNA sequencing

SNPsingle nucleotide polymorphism

SSCPSingle Strand Conformational Polymorphism

TFtranscription factor

WGDwhole genome duplication.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2011-12-12-r119 contains supplementary material, which is available to authorized users.

Caroline Pont, Florent Murat contributed equally to this work.

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Author: Caroline Pont - Florent Murat - Carole Confolent - Sandrine Balzergue - Jérôme Salse

Source: https://link.springer.com/







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