ArticleBMC genomics2023
Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 8 citations in OpenAlex.
- Multiomics analysis ofHorticulture research · 2026Article
- Pan-NLR gene family analyses decipher evolutionary dynamics, population diversity, and potential disease resistance genes in cucumber.BMC plant biology · 2026Article
- Current and future pangenomic research in cucurbit crops.Breeding science · 2025Article
- The developments and prospects of plant super-pangenomes: Demands, approaches, and applications.Plant communications · 2025Review
- Genome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in KBMC genomics · 2024Article
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14 authors at 3 institutions in 1 country.
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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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