Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri )

Frontiers in Plant Science
Xin QiaoShaoling Zhang

Abstract

Pear is an important fruit crop of the Rosaceae family and has experienced two rounds of ancient whole-genome duplications (WGDs). However, whether different types of gene duplications evolved differently after duplication remains unclear in the pear genome. In this study, we identified the different modes of gene duplication in pear. Duplicate genes derived from WGD, tandem, proximal, retrotransposed, DNA-based transposed or dispersed duplications differ in genomic distribution, gene features, selection pressure, expression divergence, regulatory divergence and biological roles. Widespread sequence, expression and regulatory divergence have occurred between duplicate genes over the 30-45 million years of evolution after the recent genome duplication in pear. The retrotransposed genes show relatively higher expression and regulatory divergence than other gene duplication modes. In contrast, WGD genes underwent a slower sequence divergence and may be influenced by abundant gene conversion events. Moreover, the different classes of duplicate genes exhibited biased functional roles. We also investigated the evolution and expansion patterns of the gene families involved in sugar and organic acid metabolism pathways, which are close...Continue Reading

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Citations

Apr 10, 2020·The Plant Journal : for Cell and Molecular Biology·Kanhu C Moharana, Thiago M Venancio
Jun 28, 2018·Functional & Integrative Genomics·Yunpeng CaoYongping Cai
Oct 2, 2020·Communications Biology·Alys M Cheatle JarvelaLeslie Pick
Sep 21, 2021·Tree Physiology·Pia Guadalupe Dominguez, Totte Niittylä
Jan 13, 2022·Genome Biology and Evolution·Zoe VanceAoife McLysaght

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

MCScanX
Python
Trimmomatic
Scipy
GOATOOLS
BLASTP
_ Calculator
NumPy
hmmscan
BEDTools

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