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.
Highlights
IntroductionGuibing Hu1,18, Junting Feng[1,18], Xu Xiang[2,18], Jiabao Wang[3,18], Jarkko Salojärvi 4,18, Chengming Liu[1,18], Zhenxian Wu 1,18, Jisen Zhang 5, Xinming Liang[6], Zide Jiang[7], Wei Liu[2], Liangxi Ou2, Jiawei Li1, Guangyi Fan[6], Yingxiao Mai[1], Chengjie Chen[1], Xingtan Zhang[5], Jiakun Zheng[1], Yanqing Zhang[1], Hongxiang Peng[8], Lixian Yao[9], Ching Man Wai[10], Xinping Luo[11], Jiaxin Fu1, Haibao Tang 5, Tianying Lan[12], Biao Lai[1], Jinhua Sun[3], Yongzan Wei 13, Huanling Li3, Jiezhen Chen[2], Xuming Huang[1], Lychee is an exotic tropical fruit with a distinct flavor
The haplotype, similar to the flow cytometry estimate, was anchored into pseudochromosomes using the physical map generated with high-throughput chromatin conformation capture (Hi-C) technology (144× coverage)
MRNA sequencing (RNA-seq) data were aligned to the reference genome, and 31,896 putative protein-coding gene models were predicted with estimated completeness of 94.8%
Summary
Guibing Hu1,18, Junting Feng[1,18], Xu Xiang[2,18], Jiabao Wang[3,18], Jarkko Salojärvi 4,18, Chengming Liu[1,18], Zhenxian Wu 1,18, Jisen Zhang 5, Xinming Liang[6], Zide Jiang[7], Wei Liu[2], Liangxi Ou2, Jiawei Li1, Guangyi Fan[6], Yingxiao Mai[1], Chengjie Chen[1], Xingtan Zhang[5], Jiakun Zheng[1], Yanqing Zhang[1], Hongxiang Peng[8], Lixian Yao[9], Ching Man Wai[10], Xinping Luo[11], Jiaxin Fu1, Haibao Tang 5, Tianying Lan[12], Biao Lai[1], Jinhua Sun[3], Yongzan Wei 13, Huanling Li3, Jiezhen Chen[2], Xuming Huang[1], Lychee is an exotic tropical fruit with a distinct flavor. 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. Lychee has been cultivated in southern China for millennia. The oldest lychee tree, ‘Songxiang’, from Fujian, China, is over 1,250 years old, and is still fruiting today. This long cultivation history has facilitated the generation of diverse lychee germplasm. Over 400 lychee cultivars are preserved at the National Lychee Germplasm Resources in Guangzhou, China
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