Long read sequencing and de novo assembly of Luffa cylindrica (L.) Roem. genome

Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid with 26 chromosomes (2n = 26) herbaceous plant, belonging to Cucurbitaceae family. L. cylindrica (L.) Roem. is a potentially commercial crop with combination of edible and medicinal value, and is worth for further study. To address the genome resources limitations of Luffa species, a chromosome-level genome of L. cylindrica (L.) Roem. was assembled and analyzed using PacBio long reads and Hi-C data. Findings: We assembled the L. cylindrica (L.) Roem. genome with a total of 133 Gb and 74 Gb of raw reads that were generated using both BGIseq500 and Pacific Bioscience (PacBio) Sequel platforms, respectively. The final draft genome assembly was approximately 669 Mb with a contig N50 of 5 Mb. The genome size was lower with the estimated genome size (737 Mb) based on k-mer analysis. We combined Hi-C data with a draft genome assembly to generate chromosome-length scaffolds. Thirteen scaffolds corresponding to the 13 chromosomes were assembled to a final size of 669 Mb with a contig N50 of 5 Mb and a scaffold N50 of 53 Mb using 1156 contigs. After redundancy removing, 416.31 Mb (62.18% of the genome) repeat sequences were detected. Subsequently, 31661 protein-coding genes with an average of 5.69 exons per gene was identified in the L. cylindrica (L.) Roem. genome using de novo methods, transcriptome data and homolog-based approaches to other species. And 27552 protein-coding genes with a percentage of 87.02% were annotated on five databases. According to phylogenetic analysis using single-copy orthologs, L. cylindrica (L.) Roem. is closely related to some Cucurbita and Cucumis species which all belong to Cucurbitaceae family, with diverging from their common ancestor approximately 28.6–67.1 million years ago. Conclusions: We achieved a high-quality genome for L. cylindrica (L.) Roem. using long-read PacBio sequencing and Hi-C auxiliary assembly technology, which represents the first chromosome-level reference genome for Luffa species. The completeness of the genome will provide high-quality genomic resources on breeding and genetic variation discovery in L. cylindrica (L.) Roem.