Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes

Frontiers in Plant Science

Plant Science

Andrea R. Gschwend¹  Bo Li¹ 

[1] Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States;

关键词: Vitis labrusca;    Vitis vinifera;    grapevine;    comparative genomics;    genetic variation;    segmental duplication;    zygosity;    adaptive evolution;   

DOI  :  10.3389/fpls.2023.1234130

 received in 2023-06-03, accepted in 2023-08-03,  发布年份 2023

来源: Frontiers

【 摘 要 】

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

【 授权许可】

Unknown   
Copyright © 2023 Li and Gschwend