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Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars
Wednesday, 2022/01/12 | 08:01:22

Guibing HuJunting FengXu XiangJiabao WangJarkko SalojärviChengming LiuZhenxian WuJisen ZhangXinming LiangZide JiangWei LiuLiangxi OuJiawei LiGuangyi FanYingxiao MaiChengjie ChenXingtan ZhangJiakun ZhengYanqing ZhangHongxiang PengLixian YaoChing Man WaiXinping LuoJiaxin FuHaibao TangTianying LanBiao LaiJinhua SunYongzan WeiHuanling LiJiezhen ChenXuming HuangQian YanXin LiuLeah K. McHaleWilliam RollingRomain GuyotDavid SankoffChunfang ZhengVictor A. AlbertRay MingHoubin ChenRui Xia & Jianguo Li

Nature Genetics 2022; 3 January 2022

Abstract

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops.

 

See https://www.nature.com/articles/s41588-021-00971-3

 

Figure 1: Assembly, composition and evolution of the lychee genome.

a, Schematic presentation of lychee fruit. Scale bar, 5 cm (left), 3 cm (right). b, Contact map of Hi-C links among 15 pseudochromosomes. c, Lychee genomic features. d, Phylogenetic and molecular clock dating analysis of the lychee genome with 13 other species, based on single-copy orthogroup data. The red diamond indicates our fossil calibration point26, and the blue diamond represents S. lycopersicum divergence time27. The light blue bars at the internodes represent 95% confidence intervals for divergence times. e, Synonymous substitution rate (Ks) density distributions of syntenic lychee paralogs and orthologs compared with other eudicot species.

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