Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

被引：245

作者：

Zhang, Xingtan ^{[1
,2
]}

Chen, Shuai ^{[1
,3
,4
]}

Shi, Longqing ^{[1
,3
,5
]}

Gong, Daping ^{[6
]}

Zhang, Shengcheng ^{[4
]}

Zhao, Qian ^{[1
,5
]}

Zhan, Dongliang ^{[7
]}

Vasseur, Liette ^{[1
,5
,8
]}

Wang, Yibin ^{[4
]}

Yu, Jiaxin ^{[4
]}

Liao, Zhenyang ^{[4
]}

Xu, Xindan ^{[4
]}

Qi, Rui ^{[4
]}

Wang, Wenling ^{[4
]}

Ma, Yunran ^{[4
]}

Wang, Pengjie ^{[9
]}

Ye, Naixing ^{[9
]}

Ma, Dongna ^{[1
]}

Shi, Yan ^{[1
]}

Wang, Haifeng ^{[1
]}

Ma, Xiaokai ^{[4
]}

Kong, Xiangrui ^{[10
]}

Lin, Jing ^{[4
]}

Wei, Liufeng ^{[1
]}

Ma, Yaying ^{[4
]}

Li, Ruoyu ^{[4
]}

Hu, Guiping ^{[1
,11
]}

He, Haifang ^{[1
]}

Zhang, Lin ^{[12
]}

Ming, Ray ^{[13
]}

Wang, Gang ^{[14
]}

Tang, Haibao ^{[4
]}

You, Minsheng ^{[1
,5
]}

机构：

[1] Fujian Agr & Forestry Univ, Coll Plant Protect, Inst Appl Ecol, State Key Lab Ecol Pest Control Fujian & Taiwan C, Fuzhou, Peoples R China

[2] Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Minist Agr,Shenzhen Branch,Genome Anal Lab, Shenzhen, Peoples R China

[3] Fujian Acad Agr Sci, Inst Rice, Fuzhou, Peoples R China

[4] Fujian Agr & Forestry Univ, Key Lab Genet, Fujian Prov Key Lab Haixia Appl Plant Syst Biol, Ctr Genom & Biotechnol, Fuzhou, Peoples R China

[5] Fujian Agr & Forestry Univ, Joint Int Res Lab Ecol Pest Control, Ministerial & Prov Joint Innovat Ctr Safety Prod, Minist Educ, Fuzhou, Peoples R China

[6] Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China

[7] Hangzhou Kaitai Biotech Co Ltd, Hangzhou, Peoples R China

[8] Brock Univ, Dept Biol Sci, St Catharines, ON, Canada

[9] Fujian Agr & Forestry Univ, Coll Hort, Key Lab Tea Sci, Fuzhou, Peoples R China

[10] Fujian Acad Agr Sci, Tea Res Inst, Fuzhou, Peoples R China

[11] Jiangxi Sericulture & Tea Res Inst, Nanchang, Jiangxi, Peoples R China

[12] Cent South Univ Forestry & Technol, Minist Educ, Key Lab Cultivat & Protect Nonwood Forest Trees, Changsha, Peoples R China

[13] Univ Illinois, Dept Plant Biol, Urbana, IL USA

[14] Chinese Acad Sci, Xishuangbanna Trop Bot Garden, CAS Key Lab Trop Forest Ecol, Mengla, Peoples R China

来源：

NATURE GENETICS | 2021年 / 53卷 / 08期

基金：

国家重点研发计划;

关键词：

GENERATION; TOOL; DNA; SELECTION; ALIGNMENT; PROGRAM; GENES; RNA;

D O I：

10.1038/s41588-021-00895-y

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Haplotype-resolved genome assembly of an Oolong tea cultivar Tieguanyin and population genomic analyses of 190 Camellia accessions provide insights into the evolutionary history of the tea plant Camellia sinensis. Tea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.

引用

页码：1250 / +

页数：23

共 69 条

[1] TEclass-a tool for automated classification of unknown eukaryotic transposable elements [J].

Abrusan, Gyorgy ;

Grundmann, Norbert ;

DeMester, Luc ;

Makalowski, Wojciech .

BIOINFORMATICS, 2009, 25 (10) :1329-1330

[2]

Banerjee B., 1992, TEA, P25, DOI DOI 10.1007/978-94-011-2326-62

[3] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[4] JBrowse: a dynamic web platform for genome visualization and analysis [J].

Buels, Robert ;

Yao, Eric ;

Diesh, Colin M. ;

Hayes, Richard D. ;

Munoz-Torres, Monica ;

Helt, Gregg ;

Goodstein, David M. ;

Elsik, Christine G. ;

Lewis, Suzanna E. ;

Stein, Lincoln ;

Holmes, Ian H. .

GENOME BIOLOGY, 2016, 17

[5] MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes [J].

Cantarel, Brandi L. ;

Korf, Ian ;

Robb, Sofia M. C. ;

Parra, Genis ;

Ross, Eric ;

Moore, Barry ;

Holt, Carson ;

Alvarado, Alejandro Sanchez ;

Yandell, Mark .

GENOME RESEARCH, 2008, 18 (01) :188-196

[6] The DWF4 gene of Arabidopsis encodes a cytochrome P450 that mediates multiple 22α-hydroxylation steps in brassinosteroid biosynthesis [J].

Choe, SW ;

Dilkes, BP ;

Fujioka, S ;

Takatsuto, S ;

Sakurai, A ;

Feldmann, KA .

PLANT CELL, 1998, 10 (02) :231-243

[7] A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 [J].

Cingolani, Pablo ;

Platts, Adrian ;

Wang, Le Lily ;

Coon, Melissa ;

Tung Nguyen ;

Wang, Luan ;

Land, Susan J. ;

Lu, Xiangyi ;

Ruden, Douglas M. .

FLY, 2012, 6 (02) :80-92

[8] The variant call format and VCFtools [J].

Danecek, Petr ;

Auton, Adam ;

Abecasis, Goncalo ;

Albers, Cornelis A. ;

Banks, Eric ;

DePristo, Mark A. ;

Handsaker, Robert E. ;

Lunter, Gerton ;

Marth, Gabor T. ;

Sherry, Stephen T. ;

McVean, Gilean ;

Durbin, Richard .

BIOINFORMATICS, 2011, 27 (15) :2156-2158

[9] De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds [J].

Dudchenko, Olga ;

Batra, Sanjit S. ;

Omer, Arina D. ;

Nyquist, Sarah K. ;

Hoeger, Marie ;

Durand, Neva C. ;

Shamim, Muhammad S. ;

Machol, Ido ;

Lander, Eric S. ;

Aiden, Aviva Presser ;

Aiden, Erez Lieberman .

SCIENCE, 2017, 356 (6333) :92-95

[10] Testing for Ancient Admixture between Closely Related Populations [J].

Durand, Eric Y. ;

Patterson, Nick ;

Reich, David ;

Slatkin, Montgomery .

MOLECULAR BIOLOGY AND EVOLUTION, 2011, 28 (08) :2239-2252

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