A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

• Published in: Molecular plant Vol. 15; no. 8; pp. 1268 - 1284
• Main Authors: Deng, Yun, Liu, Shoucheng, Zhang, Yilin, Tan, Jingsheng, Li, Xiaopeng, Chu, Xiao, Xu, Binghua, Tian, Yao, Sun, Yudong, Li, Bosheng, Xu, Yunbi, Deng, Xing Wang, He, Hang, Zhang, Xingping
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01.08.2022
• Subjects: EMS; gap-free genome; gene discovery; genic male sterility; genome-wide sequencing; mutation library; watermelon; gap-free genome; gene discovery; genic male sterility; mutation library; EMS; watermelon; genome-wide sequencing
• ISSN: 1674-2052; 1752-9867
• DOI: 10.1016/j.molp.2022.06.010

Watermelon, Citrullus lanatus, is the world’s third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon. A gap-free genome of the elite watermelon inbred line G42 was assembled, with all 22 telomeres and 11 centromeres characterized. Over 200 000 M1 seeds were generated from G42 using pollen-EMS mutagenesis, and more than 301 mutants with morphological changes were confirmed and sequenced from the sampled M1 and M2 populations. The gap-free genome and its EMS mutation library provide important resources for watermelon genetics, genomics, and improvement.