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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BMC
2023-06-01
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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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