Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding

Authors: ZHANG, YILIN - Peking University; ZHAO, MINGXIA - Peking University; TAN, JINGSHENG - Peking University; HUANG, MINGHAN - Peking University; CHU, XIAO - Peking University; LI, YAN - Peking University; HAN, XUE - Peking University; FANG, TAOHONG - Peking University; TIAN, YAO - Peking University; Jarret, Robert - Bob; LU, DONGDONG - Peking University; CHEN, YIJUN - Peking University; XUE, LIFANG - Peking University; LI, XIAONI - Peking University; QIN, GUOCHEN - Peking University; LI, BOSHENG - Peking University; SUN, YUDONG - Peking University; WANG DENG, XING - Peking University; DENG, YUN - Peking University; ZHANG, XINGPING - Peking University; HE, HANG - Peking University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2024
Publication Date: 7/8/2024
Citation: Zhang, Y., Zhao, M., Tan, J., Huang, M., Chu, X., Li, Y., Han, X., Fang, T., Tian, Y., Jarret, R.L., Lu, D., Chen, Y., Xue, L., Li, X., Qin, G., Li, B., Sun, Y., Wang Deng, X., Deng, Y., Zhang, X., He, H. 2024. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics. https://doi.org/10.1038/s41588-024-01823-6.
DOI: https://doi.org/10.1038/s41588-024-01823-6

Interpretive Summary: In order to address problems associated with maintaining the current levels of watermelon production that are threatened by insect pests, diseases and loses that occur after harvest, new watermelon varieties are continually under development. The development of these new varieties depends on research that identifies new characteristics that can then be introduced into watermelon cultivars. These characteristics might include, for example, resistance to diseases or insect pests, the ability to produce fruit under extreme temperatures or lack of water, etc. Some desired traits are not available in other watermelon lines and so efforts often turn to the use of species that are related to watermelon that possess desirable traits. These related species are called watermelon's crop wild relatives (CWR). This study examined the genetic makeup of 6 species (CWR) that are related to watermelon and that might be utilized to improve watermelon production. The DNA of each CWR was completely sequenced and then compared with all other watermelon CWR and the cultivated watermelon. The results yielded valuable information on the presence or absence of various traits in the CWR and examined their potential for use in supporting efforts to develop new watermelon varieties.

Technical Abstract: In order to more completely detect and characterize the genetic diversity and complexities within the cucurbit genus Citrullus, we constructed the Telomere-to-Telomer (T2T) assemblies of 27 genotypes, representing all seven Citrullus species. The T2T super-pangenome adds 399.2 Mb and 11,225 genes to the published reference watermelon genome, T2T-G42. 35,546,180 SNPs and 461,987 SVs were identified. These data provided valuable information on watermelon domestication and the evolution of traits such as bitterness and sugar content. The SVs identified in C. lanatus were inherited not only from C. lanatus subsp. cordophanus, but also from C. mucosospermus. Multi-disease resistance was successfully introduced from the wild relatives into C. lanatus, as confirmed by genome analysis. In summary, this study provides a comprehensive resource to be used in efforts to understand the diversity and complexity of the watermelon genome and to facilitate the study and use of watermelon’s wild relatives for the improvement of the cultivated crop.