Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata.

Abstract

Objectives: Hygroryza aristata, an aquatic plant native to Southeast Asia, shows a high degree of adaptability to aquatic environments. H. aristata, which belongs to the Oryzeae tribe and is closely related to rice (Oryza sativa), holds potential for crop improvement, particularly in flood tolerance. This study aimed to sequence and assemble the genome of H. aristata.

Data description: We assembled the genome of H. aristata using 31.91 Gb of Pacific Biosciences (PacBio) High-fidelity (HiFi) data and 22.36 Gb of ultra long Oxford Nanopore Technology (ONT) data, resulting in two gap-free haplotype genomes, hap1 (349.74 Mb) and hap2 (347.98 Mb), each with 12 chromosomes and 23 telomeres. The continuity of chromosomes was supported by High-throughput chromosome conformation capture (Hi-C) data. The assemblies demonstrated high completeness, with > 99.8% of coverage rates, 98.4% of Benchmarking Universal Single-Copy Orthologs (BUSCO) scores, and > 11.0 of Long Terminal Repeat Assembly Index (LAI) scores per haplotype. RNA sequencing (RNA-seq) data (176.06 Gb) of six tissues was generated for genome annotation, identifying 39,139 and 38,746 protein-coding genes in hap1 and hap2, respectively.