Cargando…
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars
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 i...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8755541/ https://www.ncbi.nlm.nih.gov/pubmed/34980919 http://dx.doi.org/10.1038/s41588-021-00971-3 |
_version_ | 1784632399894675456 |
---|---|
author | Hu, Guibing Feng, Junting Xiang, Xu Wang, Jiabao Salojärvi, Jarkko Liu, Chengming Wu, Zhenxian Zhang, Jisen Liang, Xinming Jiang, Zide Liu, Wei Ou, Liangxi Li, Jiawei Fan, Guangyi Mai, Yingxiao Chen, Chengjie Zhang, Xingtan Zheng, Jiakun Zhang, Yanqing Peng, Hongxiang Yao, Lixian Wai, Ching Man Luo, Xinping Fu, Jiaxin Tang, Haibao Lan, Tianying Lai, Biao Sun, Jinhua Wei, Yongzan Li, Huanling Chen, Jiezhen Huang, Xuming Yan, Qian Liu, Xin McHale, Leah K. Rolling, William Guyot, Romain Sankoff, David Zheng, Chunfang Albert, Victor A. Ming, Ray Chen, Houbin Xia, Rui Li, Jianguo |
author_facet | Hu, Guibing Feng, Junting Xiang, Xu Wang, Jiabao Salojärvi, Jarkko Liu, Chengming Wu, Zhenxian Zhang, Jisen Liang, Xinming Jiang, Zide Liu, Wei Ou, Liangxi Li, Jiawei Fan, Guangyi Mai, Yingxiao Chen, Chengjie Zhang, Xingtan Zheng, Jiakun Zhang, Yanqing Peng, Hongxiang Yao, Lixian Wai, Ching Man Luo, Xinping Fu, Jiaxin Tang, Haibao Lan, Tianying Lai, Biao Sun, Jinhua Wei, Yongzan Li, Huanling Chen, Jiezhen Huang, Xuming Yan, Qian Liu, Xin McHale, Leah K. Rolling, William Guyot, Romain Sankoff, David Zheng, Chunfang Albert, Victor A. Ming, Ray Chen, Houbin Xia, Rui Li, Jianguo |
author_sort | Hu, Guibing |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8755541 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-87555412022-01-26 Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars Hu, Guibing Feng, Junting Xiang, Xu Wang, Jiabao Salojärvi, Jarkko Liu, Chengming Wu, Zhenxian Zhang, Jisen Liang, Xinming Jiang, Zide Liu, Wei Ou, Liangxi Li, Jiawei Fan, Guangyi Mai, Yingxiao Chen, Chengjie Zhang, Xingtan Zheng, Jiakun Zhang, Yanqing Peng, Hongxiang Yao, Lixian Wai, Ching Man Luo, Xinping Fu, Jiaxin Tang, Haibao Lan, Tianying Lai, Biao Sun, Jinhua Wei, Yongzan Li, Huanling Chen, Jiezhen Huang, Xuming Yan, Qian Liu, Xin McHale, Leah K. Rolling, William Guyot, Romain Sankoff, David Zheng, Chunfang Albert, Victor A. Ming, Ray Chen, Houbin Xia, Rui Li, Jianguo Nat Genet Article 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. Nature Publishing Group US 2022-01-03 2022 /pmc/articles/PMC8755541/ /pubmed/34980919 http://dx.doi.org/10.1038/s41588-021-00971-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Hu, Guibing Feng, Junting Xiang, Xu Wang, Jiabao Salojärvi, Jarkko Liu, Chengming Wu, Zhenxian Zhang, Jisen Liang, Xinming Jiang, Zide Liu, Wei Ou, Liangxi Li, Jiawei Fan, Guangyi Mai, Yingxiao Chen, Chengjie Zhang, Xingtan Zheng, Jiakun Zhang, Yanqing Peng, Hongxiang Yao, Lixian Wai, Ching Man Luo, Xinping Fu, Jiaxin Tang, Haibao Lan, Tianying Lai, Biao Sun, Jinhua Wei, Yongzan Li, Huanling Chen, Jiezhen Huang, Xuming Yan, Qian Liu, Xin McHale, Leah K. Rolling, William Guyot, Romain Sankoff, David Zheng, Chunfang Albert, Victor A. Ming, Ray Chen, Houbin Xia, Rui Li, Jianguo Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title | Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title_full | Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title_fullStr | Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title_full_unstemmed | Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title_short | Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
title_sort | two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8755541/ https://www.ncbi.nlm.nih.gov/pubmed/34980919 http://dx.doi.org/10.1038/s41588-021-00971-3 |
work_keys_str_mv | AT huguibing twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT fengjunting twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT xiangxu twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT wangjiabao twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT salojarvijarkko twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT liuchengming twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT wuzhenxian twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT zhangjisen twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT liangxinming twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT jiangzide twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT liuwei twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT ouliangxi twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT lijiawei twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT fanguangyi twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT maiyingxiao twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT chenchengjie twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT zhangxingtan twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT zhengjiakun twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT zhangyanqing twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT penghongxiang twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT yaolixian twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT waichingman twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT luoxinping twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT fujiaxin twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT tanghaibao twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT lantianying twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT laibiao twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT sunjinhua twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT weiyongzan twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT lihuanling twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT chenjiezhen twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT huangxuming twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT yanqian twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT liuxin twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT mchaleleahk twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT rollingwilliam twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT guyotromain twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT sankoffdavid twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT zhengchunfang twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT albertvictora twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT mingray twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT chenhoubin twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT xiarui twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars AT lijianguo twodivergenthaplotypesfromahighlyheterozygouslycheegenomesuggestindependentdomesticationeventsforearlyandlatematuringcultivars |