Improved chromosome-level genome and annotation data for a leafy vegetable water spinach (Ipomoea aquatica)

Abstract

Water spinach (Ipomoea aquatica Forssk.) is an important green leafy vegetable in Asia, with high content of dietary fiber, minerals, and vitamins. The genome sequence of water spinach cv. HNUWS001 was published in 2021 with PacBio and Illumina sequences. However, this assembly showed low contig continuity and low BUSCO complete rate for the genes. Here, we reported a high-quality chromosome-level reference genome for water spinach by integrating PacBio high-fidelity (HiFi) sequencing and Hi-C technology. The water spinach assembly was improved 492.2 Mb in size, with chromosome anchoring rate of 96.5%, contig N50 size of 23.5 Mb, and BUSCO complete rate of 99%. Telomeric repeat analysis indicates that 13 of the 15 pseudo-chromosomes have both-end telomeric repeats, including 4 gapless and telomere to telomere pseudo-chromosomes. We identified 36,014 protein-coding genes in the improved water spinach assembly, with BUSCO complete rate of 99.0%, and 88.5% of genes were functionally annotated. In addition, we identified 8,853 rRNA genes in our assembly, with 5S, 5.8S, 18S, and 28S rRNA genes were 5,235, 1,199, 1,227, and 1,192, respectively. Besides, evolution analysis based on the improved gene set suggested a whole genome triplication (WGT) event that occurred in water spinach, not the previously reported whole genome duplication (WGD) event. The improved genome assembly has a 14-fold increase in contig N50 size, a 15.5% increase in chromosome anchoring rate, and a 3.1% increase in BUSCO complete rate of the gene set, and corrected 6 pseudo-chromosomes that with some incorrectly clustered, ordered, or orientated contigs in previous study. The results of water spinach assembly and annotation provides a valuable resource for genetic studies and will facilitate future research aimed at improving agronomic traits.