S01 - Session P2 - High quality genomes of Luffa cylindrica and L. acutangula

Authors: Haibin Wu *, Gangjun Zhao, Jianning Luo, Junqiu Chen, Hao Gong, Junxing Li, Xiaoli He, Shaobo Luo, Xiaoming Zheng, Xiaoxi Liu

Sponge gourd, also called luffa, is an important cultivated vegetable and medicinal plant in the family Cucurbitaceae. There are nine different species in the Luffa genus, of which only L. acutangula (L.) Roxb. and L. cylindrica (L.) Roem. are domesticated. In this study, the draft genome sequences of the L. cylindrica inbred line P93075 and L. acutangula inbred line S1174 were analyzed. Using Illumina, PacBio, and 10× genomic sequencing techniques as well as new assembly techniques, such as FALCON and chromatin interaction mapping (Hi-C), two chromosome-scale genomes were generated. The assembled 656.19 Mb genome of P93075 was obtained with an N50 scaffold of 48.76 Mb and 25,508 protein-coding gene loci were identified. The 776.49 Mb genome of S1174 was assembled with an N50 scaffold of 54.64 Mb and has 27,405 genes. The repetitive sequences accounted for 63.8% of the P93075 genome and 65.7% of S1174, which are major contributors to the expansion of the sponge gourd genome. In terms of genome and protein-coding genes, S1174 has 120.3 Mb and 1897 more protein-coding genes than P93075. Although they are quite different, L. acutangula and L. cylindrica can still hybridize and produce offspring, with the F1 generation of crosses having low pollen fertility. According to a phylogenetic analysis of conserved genes, L. cylindrica lineage diverged from the L. acutangula lineage approximately 8.2 (4.5n17.7) million years ago. Meanwhile, many genes that respond to biotic and abiotic stresses were lineage-specific or expanded in the L. cylindrica genome, as demonstrated by the presence of 462 NBS-LRR genes, many more than those contained in the genomes of other cucurbit species. These results are consistent with the high stress resistance of sponge gourd. Collectively, our study provides insights into exploring genome evolution and serves as a valuable reference for genetic improvement of sponge gourd.