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Research Project: Genomics and Genetic Improvement of Disease Resistance and Horticultural Characteristics of Watermelon, Broccoli, and Leafy Brassicas

Location: Vegetable Research

Title: Pan-genomes of the citrullus species

item WU, SHAN - Boyce Thompson Institute
item GAO, LEI - Boyce Thompson Institute
item MENDIETA, JOHN - Boyce Thompson Institute
item GUO, SHAOGUI - National Engineering Center For Vegetables
item SUN, HONGHE - National Engineering Center For Vegetables
item XU, YONG - National Engineering Center For Vegetables
item Kousik, Chandrasekar - Shaker
item Wechter, William - Pat
item Levi, Amnon
item FEI, ZHANGJUN - Boyce Thompson Institute

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/18/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Watermelon (Citrullus lanatus) is among the most important vegetable crops in the world. It belongs to the Citrullus (2n=2x=22) genus, which includes six other species, namely egusi watermelon (C. mucosospermus), citron watermelon (C. amarus), colocynth (C. colocynthis), C. ecirrhosus, C. rehmii and C. naudinianus. To maximize the capture of genome variations within and among these Citrullus species and to identify novel agronomically important alleles for facilitating watermelon breeding, we are constructing pan-genomes of the Citrullus species. We have been generating high-quality reference genomes from selected individuals of four Citrullus species, including two C. lanatus accessions, two C. amarus and one C. colocynthis whose genome assemblies and annotations are finished, and one in the process for C. mucosospermus. We also generated whole genome resequencing data from more than 400 additional accessions of these four species, which are being de novo assembled for each accession. A pan-genome for each of the four species will be constructed by combining the reference genome(s) and de novo assembled novel non-redundant sequences. Presence-absence variations (PAVs) of protein-coding genes will be analyzed, and collections of core and distributed gene sets for each species will be identified. Comparative analysis of the four pan-genomes will be performed to highlight syntenic regions and species-specific variations. The Citrullus pan-genomes and the identified PAVs will enable us to trace the distribution of functionally important alleles and gain insights into watermelon evolution, domestication and introgression, and provide an important resource to facilitate the mining of natural variation in Citrullus for scientific studies and the improvement of watermelon.