Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

Genome Biology
Xin QiaoAndrew H Paterson

Abstract

The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in...Continue Reading

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Citations

Nov 17, 2019·International Journal of Molecular Sciences·Wei ZhaoJing Liu
Jan 29, 2020·Genome Biology and Evolution·Eduard Ocaña-PallarèsCrisanto Gutierrez
Apr 7, 2020·The FEBS Journal·Shelley D Copley
May 22, 2020·The Plant Journal : for Cell and Molecular Biology·Merijn H L KerstensKlaas Bouwmeester
Jul 12, 2020·The Plant Journal : for Cell and Molecular Biology·Woo-Jong HongKi-Hong Jung
Jun 17, 2020·Genome Biology and Evolution·Bikash ShresthaRobert K Jansen
Apr 26, 2020·Molecular Genetics and Genomics : MGG·Ana Paula Zotta MotaMaria Fatima Grossi-de-Sa
Aug 10, 2019·Frontiers in Plant Science·Juan ViruelIlia J Leitch
Oct 28, 2019·Horticulture Research·Fei ChenLiangsheng Zhang
Oct 21, 2020·Nature Communications·Fu-Sheng YangJian-Feng Mao
Nov 27, 2020·Frontiers in Genetics·Jeremy E CoateJeff J Doyle
Dec 22, 2020·PeerJ·Xianwen MengJiuli Wang
Mar 18, 2020·Computational and Structural Biotechnology Journal·Federico Scossa, Alisdair R Fernie
Nov 21, 2020·The Plant Journal : for Cell and Molecular Biology·Hui LiuZong-Ming Max Cheng
Dec 31, 2020·Plant Direct·Chi ZhangFeng Chen

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

custom
GOATOOLS
OrthoFinder
DupGen
MAFFT
Perl script
Ensembl
DupGen finder
PAL2NAL
_ Calculator

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