Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding

被引：7

作者：

Zhang, Yilin ^{[1
,2
,3
]}

Zhao, Mingxia ^{[1
]}

Tan, Jingsheng ^{[1
]}

Huang, Minghan ^{[2
,3
]}

Chu, Xiao ^{[1
]}

Li, Yan ^{[1
]}

Han, Xue ^{[1
]}

Fang, Taohong ^{[1
]}

Tian, Yao ^{[1
]}

Jarret, Robert ^{[4
]}

Lu, Dongdong ^{[1
]}

Chen, Yijun ^{[1
]}

Xue, Lifang ^{[1
]}

Li, Xiaoni ^{[1
]}

Qin, Guochen ^{[1
]}

Li, Bosheng ^{[1
]}

Sun, Yudong ^{[5
]}

Deng, Xing Wang ^{[1
,2
,3
]}

Deng, Yun ^{[1
]}

Zhang, Xingping ^{[1
]}

He, Hang ^{[1
,2
,3
]}

机构：

[1] Peking Univ, Inst Adv Agr Sci, Natl Key Lab Wheat Improvement, Shandong Lab Adv Agr Sci Weifang, Weifang, Peoples R China

[2] Peking Univ, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

[3] Peking Univ, Sch Life Sci, Beijing, Peoples R China

[4] Plant Genet Resource Unit, Griffin, GA USA

[5] Huaiyin Inst Agr Sci Xuhuai Reg Jiangsu, Vegetable Res & Dev Ctr, Huaian, Peoples R China

来源：

NATURE GENETICS | 2024年

关键词：

MULTIPLE SEQUENCE ALIGNMENT; LEVEL EXPRESSION; F-1; HYBRIDS; GENOME; ANNOTATION; LANATUS; PROGRAM; TOMATO;

D O I：

10.1038/s41588-024-01823-6

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.

引用

页码：1750 / 1761

页数：20

共 108 条

[11] eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Cantalapiedra, Carlos P.
Hernandez-Plaza, Ana
Letunic, Ivica
Bork, Peer
Huerta-Cepas, Jaime
[J]. MOLECULAR BIOLOGY AND EVOLUTION, 2021, 38 (12) : 5825 - 5829
[12] Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Cartney, Ann M. Mc
Shafin, Kishwar
Alonge, Michael
Bzikadze, Andrey, V
Formenti, Giulio
Fungtammasan, Arkarachai
Howe, Kerstin
Jain, Chirag
Koren, Sergey
Logsdon, Glennis A.
Miga, Karen H.
Mikheenko, Alla
Paten, Benedict
Shumate, Alaina
Soto, Daniela C.
Sovic, Ivan
Wood, Jonathan Md
Zook, Justin M.
Phillippy, Adam M.
Rhie, Arang
[J]. NATURE METHODS, 2022, 19 (06) : 687 - +
[13] An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes
Castanera, Raul
Ruggieri, Valentino
Pujol, Marta
Garcia-Mas, Jordi
Casacuberta, Josep M.
[J]. FRONTIERS IN PLANT SCIENCE, 2020, 10
[14] tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Chan, Patricia P.
Lin, Brian Y.
Mak, Allysia J.
Lowe, Todd M.
[J]. NUCLEIC ACIDS RESEARCH, 2021, 49 (16) : 9077 - 9096
[15] fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, Shifu
Zhou, Yanqing
Chen, Yaru
Gu, Jia
[J]. BIOINFORMATICS, 2018, 34 (17) : 884 - 890
[16] Haplotype-resolved assembly of diploid genomes without parental data
Cheng, Haoyu
Jarvis, Erich D.
Fedrigo, Olivier
Koepfli, Klaus-Peter
Urban, Lara
Gemmell, Neil J.
Li, Heng
[J]. NATURE BIOTECHNOLOGY, 2022, 40 (09) : 1332 - +
[17] Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, Haoyu
Concepcion, Gregory T.
Feng, Xiaowen
Zhang, Haowen
Li, Heng
[J]. NATURE METHODS, 2021, 18 (02) : 170 - +
[18] Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology
Chomicki, Guillaume
Schaefer, Hanno
Renner, Susanne S.
[J]. NEW PHYTOLOGIST, 2020, 226 (05) : 1240 - 1255
[19] Twelve years of SAMtools and BCFtools
Danecek, Petr
Bonfield, James K.
Liddle, Jennifer
Marshall, John
Ohan, Valeriu
Pollard, Martin O.
Whitwham, Andrew
Keane, Thomas
McCarthy, Shane A.
Davies, Robert M.
Li, Heng
[J]. GIGASCIENCE, 2021, 10 (02):
[20] A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding
Deng, Yun
Liu, Shoucheng
Zhang, Yilin
Tan, Jingsheng
Li, Xiaopeng
Chu, Xiao
Xu, Binghua
Tian, Yao
Sun, Yudong
Li, Bosheng
Xu, Yunbi
Deng, Xing Wang
He, Hang
Zhang, Xingping
[J]. MOLECULAR PLANT, 2022, 15 (08) : 1268 - 1284

← 1 2 3 4 5 6 7 8 9 10 →