Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

被引：35

作者：

Jia, Kai-Hua ^{[1
]}

Liu, Hui ^{[1
]}

Zhang, Ren-Gang ^{[2
]}

Xu, Jie ^{[1
]}

Zhou, Shan-Shan ^{[1
]}

Jiao, Si-Qian ^{[1
]}

Yan, Xue-Mei ^{[1
]}

Tian, Xue-Chan ^{[1
]}

Shi, Tian-Le ^{[1
]}

Luo, Hang ^{[1
]}

Li, Zhi-Chao ^{[1
]}

Bao, Yu-Tao ^{[1
]}

Nie, Shuai ^{[1
]}

Guo, Jing-Fang ^{[1
]}

Porth, Ilga ^{[3
]}

El-Kassaby, Yousry A. ^{[4
]}

Wang, Xiao-Ru ^{[1
,5
]}

Chen, Charles ^{[6
]}

Van de Peer, Yves ^{[7
,8
,9
,10
]}

Zhao, Wei ^{[1
,5
]}

Mao, Jian-Feng ^{[1
]}

机构：

[1] Beijing Forestry Univ, Coll Biol Sci & Technol, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Natl Engn Lab Tree Breeding,Minist Educ,Key Lab G, Beijing 100083, Peoples R China

[2] Ori Shandong Gene Sci & Technol Co Ltd, Weifang 261000, Shandong, Peoples R China

[3] Univ Laval, Fac Foresterie Geog & Geomat, Dept Sci Bois & Foret, Quebec City, PQ G1V 0A6, Canada

[4] Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1Z4, Canada

[5] Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-0187 Umea, Sweden

[6] Oklahoma State Univ, Noble Res Ctr 246, Dept Biochem & Mol Biol, Stillwater, OK 74078 USA

[7] Univ Ghent, Dept Plant Biotechnol & Bioinformat, Ghent, Belgium

[8] VIB Ctr Plant Syst Biol, B-9052 Ghent, Belgium

[9] Univ Pretoria, Ctr Microbial Ecol & Genom, Dept Biochem Genet & Microbiol Genet, Private Bag X20, ZA-0028 Pretoria, South Africa

[10] Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Coll Hort, Nanjing 210095, Peoples R China

来源：

HORTICULTURE RESEARCH | 2021年 / 8卷 / 01期

基金：

欧洲研究理事会;

关键词：

TRANSPOSABLE ELEMENTS; GENE DUPLICATION; SEQUENCE; ANNOTATION; POLYPLOIDY; ANCIENT; DIVERSIFICATION; IDENTIFICATION; CONSEQUENCES; DIVERGENCE;

D O I：

10.1038/s41438-021-00614-y

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the gamma event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

引用

页数：15

共 115 条

[91] The Arabidopsis Information Resource (TAIR): gene structure and function annotation [J].