Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
Kai-Hua Jia1 , Hui Liu1 , Ren-Gang Zhang2 , Jie Xu1 , Shan-Shan Zhou1 , Si-Qian Jiao1 , Xue-Mei Yan1 , Xue-Chan Tian1 , Tian-Le Shi1 , Hang Luo1 , Zhi-Chao Li1 , Yu-Tao Bao1 , Shuai Nie1 , Jing-Fang Guo1 , Ilga Porth3 , Yousry A. El-Kassaby4 , Xiao-Ru Wang1,5 , Charles Chen6 , Yves Van de Peer7,8,9,10 , Jian-Feng Mao 1, , Wei Zhao,1,5,
1Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China 2Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang 261000 Shandong, China 3Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec City, QC G1V 0A6, Canada 4Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 5Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden 6Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, USA 7Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium 8VIB Center for Plant Systems Biology, 9052 Ghent, Belgium 9Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa 10College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China *Corresponding author. E-mail: jianfeng.mao@bjfu.edu.cn,zhaowei.nice@gmail.com
Received: 07 Feb 2021 Revised: 12 May 2021 Accepted: 20 May 2021 Published online: 01 Sep 2021
Abstract
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 γ 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.
, Wei Zhao,1,5 ,
