The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

• Published in: Nature communications Vol. 10; no. 1; pp. 5158 - 12
• Main Authors: Xie, Dasen, Xu, Yuanchao, Wang, Jinpeng, Liu, Wenrui, Zhou, Qian, Luo, Shaobo, Huang, Wu, He, Xiaoming, Li, Qing, Peng, Qingwu, Yang, Xueyong, Yuan, Jiaqing, Yu, Jigao, Wang, Xiyin, Lucas, William J., Huang, Sanwen, Jiang, Biao, Zhang, Zhonghua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.11.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/39; 38/43; 45/23; 45/91; 631/181/2474; 631/208/212/748; 631/208/457/649; 631/449/1870; Biological evolution; Chromosomes; Cucurbita; Cucurbitaceae; Cucurbitaceae - genetics; Domestication; Economic importance; Evolution; Evolution, Molecular; Fruit - anatomy & histology; Fruit - genetics; Fruit crops; Fruits; Gene mapping; Genetic diversity; Genetic Variation; Genetics; Genetics, Population; Genome Size; Genome, Plant; Genomes; Germplasm; Gourds; Humanities and Social Sciences; Karyotype; Karyotypes; Mapping; Molecular Sequence Annotation; multidisciplinary; Nucleotide sequence; Organ Size - genetics; Phylogeny; Population genetics; Science; Science (multidisciplinary); Waxes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-13185-3

The botanical family Cucurbitaceae includes a variety of fruit crops with global or local economic importance. How their genomes evolve and the genetic basis of diversity remain largely unexplored. In this study, we sequence the genome of the wax gourd ( Benincasa hispida ), which bears giant fruit up to 80 cm in length and weighing over 20 kg. Comparative analyses of six cucurbit genomes reveal that the wax gourd genome represents the most ancestral karyotype, with the predicted ancestral genome having 15 proto-chromosomes. We also resequence 146 lines of diverse germplasm and build a variation map consisting of 16 million variations. Combining population genetics and linkage mapping, we identify a number of regions/genes potentially selected during domestication and improvement, some of which likely contribute to the large fruit size in wax gourds. Our analyses of these data help to understand genome evolution and function in cucurbits. Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.