Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae)

The New Phytologist
Huirun HuangStephen I Wright

Abstract

Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral ...Continue Reading

References

Nov 10, 2000·Science·M Lynch, J S Conery
Nov 28, 2000·Annual Review of Genetics·S P Otto, J Whitton
Jul 2, 2004·Nature·Patricia J WittkoppAndrew G Clark
Jun 22, 2005·Cellular and Molecular Life Sciences : CMLS·P J Wittkopp
Feb 19, 2008·Nature Genetics·Patricia J WittkoppAndrew G Clark
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Nov 21, 2009·The New Phytologist·James A Birchler, Reiner A Veitia
Apr 1, 2010·Genome Research·C Joel McManusPatricia J Wittkopp
May 7, 2010·Genome Research·J J EmersonWen-Hsiung Li
Jul 21, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·J J Emerson, Wen-Hsiung Li
Aug 21, 2010·Evolution; International Journal of Organic Evolution·Kelly RobertsonBoris Igić
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
May 14, 2011·Molecular Ecology Resources·Laurent Excoffier, Heidi E L Lischer
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Mar 14, 2012·The New Phytologist·Hui-Run HuangXue-Jun Ge
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Riet De SmetYves Van de Peer
Jun 25, 2013·Molecular Biology and Evolution·Bernhard SchaefkeWen-Hsiung Li
Jan 31, 2014·Methods in Molecular Biology·James A Birchler, Reiner A Veitia
Feb 28, 2014·BMC Genomics·Tae-Ho LeeAndrew H Paterson
Apr 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Margaret R WoodhouseXiaowu Wang
May 2, 2014·Molecular Biology and Evolution·Ammon ThompsonHarold H Zakon
Jul 23, 2014·American Journal of Botany·Douglas E SoltisPamela S Soltis
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Feb 19, 2015·Proceedings of the National Academy of Sciences of the United States of America·Gavin M DouglasStephen I Wright
Apr 25, 2015·Molecular Biology and Evolution·Jean-Francois Gout, Michael Lynch
Dec 15, 2011·Chemometrics and Intelligent Laboratory Systems : an International Journal Sponsored by the Chemometrics Society·Aaron M Goodpaster, Michael A Kennedy
Sep 9, 2015·Genome Biology·James A TimmonsIain J Gallagher
Jan 20, 2016·Molecular Biology and Evolution·Brian P H MetzgerPatricia J Wittkopp
Jun 1, 2004·The New Phytologist·Barbara K Mable

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