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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #400291
Research Project: Characterization of Host Resistance and Biology of Diseases and Nematodes in Vegetable Crops

Location: Vegetable Research

Title: A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication

Author
item WU, SHAN - Boyce Thompson Institute
item SUN, HONGHE - Cornell University
item GAO, LEI - Boyce Thompson Institute
item BRANHAM, SANDRA - Clemson University
item MCGREGOR, CECILIA - University Of Georgia
item XU, YONG - Beijing Academy Of Agricultural Sciences
item Kousik, Chandrasekar - Shaker
item WECHTER, W. PATRICK - Clemson University
item Levi, Amnon
item FEI, ZHANGJUN - Boyce Thompson Institute

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/25/2023
Publication Date: 9/1/2023
Citation: Wu, S., Sun, H., Gao, L., Branham, S., Mcgregor, C., Xu, Y., Kousik, C.S., Wechter, W., Levi, A., Fei, Z. 2023. A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnology Journal. 2023. https://doi.org/10.1111/pbi.14120.
DOI: https://doi.org/10.1111/pbi.14120.

Interpretive Summary: Watermelon is an important vegetable crop grown in 44 states in the U.S.A. Wild relatives of watermelon collected from different parts of the world are important resources for watermelon breeding especially because they posses resistance to important diseases and pests that attack cultivated watermelon. USDA researchers in Charleston, SC in collaboration with other researchers have developed high-quality genomes of three wild species of watermelon that will be useful in breeding watermelons for resistance to diseases and pests. The researchers also developed a watermelon super-pan genome covering four watermelon species that will serve as a valuable resource for breeding and further biological discovery. This information will be useful to seed company plant breeders, University researchers, extension agents and USDA scientists.

Technical Abstract: Sweet watermelon (Citrullus lanatus subsp. vulgaris) is among the most important vegetable crops in the world. Wild relatives are important resources for watermelon breeding. Here we report high-quality reference genomes of three wild watermelons, C. mucosospermus, C. amarus and C. colocynthis, and the divergence and genome evolution of different Citrullus species. Using genomic data from 547 watermelon accessions spanning four Citrullus species, we construct a super-pangenome to represent the Citrullus gene repertoire and provide a catalogue of orthologous relationships among species. Gene presence-absence variation analysis uncovers many disease resistant genes that are missing in cultivated watermelons, as well as genes with significantly different occurrence frequencies between populations that might underlie watermelon evolution and domestication. We revisit watermelon domestication using the recently identified wild progenitor, Kordofan melon, which provides insights into the domestication of fruit bitterness, sweetness and flesh coloration. The Citrullus super-pangenome provides a valuable resource for breeding and biological discovery, and our comparative genomic analyses shed additional lights on watermelon evolution and domestication.