Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection

Abstract The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protei...

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Main Authors: Yang Sun, Dou-Rong Kou, Yan Li, Jiang-Ping Ni, Jing Wang, Yong-Mei Zhang, Qing-Nan Wang, Bin Jiang, Xu Wang, Yue-Xin Sun, Xin-Tong Xu, Xiao-Juan Tan, Yong-Jun Zhang, Xiang-dong Kong
Format: Article
Language:English
Published: BMC 2023-06-01
Series:BMC Genomics
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Online Access:https://doi.org/10.1186/s12864-023-09443-w
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author Yang Sun
Dou-Rong Kou
Yan Li
Jiang-Ping Ni
Jing Wang
Yong-Mei Zhang
Qing-Nan Wang
Bin Jiang
Xu Wang
Yue-Xin Sun
Xin-Tong Xu
Xiao-Juan Tan
Yong-Jun Zhang
Xiang-dong Kong
author_facet Yang Sun
Dou-Rong Kou
Yan Li
Jiang-Ping Ni
Jing Wang
Yong-Mei Zhang
Qing-Nan Wang
Bin Jiang
Xu Wang
Yue-Xin Sun
Xin-Tong Xu
Xiao-Juan Tan
Yong-Jun Zhang
Xiang-dong Kong
author_sort Yang Sun
collection DOAJ
description Abstract The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
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spelling doaj.art-6a064b3540884597a974d45d1c5103f32023-06-18T11:07:29ZengBMCBMC Genomics1471-21642023-06-0124111410.1186/s12864-023-09443-wPan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selectionYang Sun0Dou-Rong Kou1Yan Li2Jiang-Ping Ni3Jing Wang4Yong-Mei Zhang5Qing-Nan Wang6Bin Jiang7Xu Wang8Yue-Xin Sun9Xin-Tong Xu10Xiao-Juan Tan11Yong-Jun Zhang12Xiang-dong Kong13Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityJiguangGene Biotechnology Co. LtdKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal UniversityLaboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesJiguangGene Biotechnology Co. LtdAbstract The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.https://doi.org/10.1186/s12864-023-09443-wCitrullus genusPan-genomePresence or absence variationRGASelectionGWAS
spellingShingle Yang Sun
Dou-Rong Kou
Yan Li
Jiang-Ping Ni
Jing Wang
Yong-Mei Zhang
Qing-Nan Wang
Bin Jiang
Xu Wang
Yue-Xin Sun
Xin-Tong Xu
Xiao-Juan Tan
Yong-Jun Zhang
Xiang-dong Kong
Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
BMC Genomics
Citrullus genus
Pan-genome
Presence or absence variation
RGA
Selection
GWAS
title Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
title_full Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
title_fullStr Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
title_full_unstemmed Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
title_short Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection
title_sort pan genome of citrullus genus highlights the extent of presence absence variation during domestication and selection
topic Citrullus genus
Pan-genome
Presence or absence variation
RGA
Selection
GWAS
url https://doi.org/10.1186/s12864-023-09443-w
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