Haplotype-Resolved and Gap-Free Genome of a Floating Aquatic Plant from the Oryzeae Tribe, Hygroryza aristata

Hygroryza aristata (Retz.) Nees ex Wight & Arn. is a floating aquatic plant. Genomic DNA and RNA samples of H. aristata were extracted from plants clonally propagated from a single individual. Long-read sequencing of PacBio HiFi and ultra-long (UL) ONT (read lengths > 100 kb), and short-read sequencing of Hi-C, WGS, and RNA-seq, were performed. 

For genome assembly, 31.91 Gb of PacBio HiFi and 22.36 Gb of UL-ONT sequencing data sets were utilized. Assembly was conducted using HiFiAsm (v0.20.0-r639) under HiFi + UL-ONT mode with the following parameters: -l 3 -r 5 -a 6 -n 10 --ctg-n 10 -w 63 -k 63. Chromosome IDs and strand directions were determined by aligning the assemblies to the rice (O. sativa) genome. The resulting assemblies of unphased two haplotypes, designated as hap1 and hap2, were obtained.

Both hap1 and hap2 are complete genomes, each comprising 12 chromosomes with genome sizes of 349.74 Mb and 347.98 Mb, respectively. Notably, both haplotypes are gap-free. Telomere detection using Seqtk telo (v1.4-r122) revealed that each haplotype contains 23 telomeres. In conclusion, this study presents a haplotype-resolved and gap-free genome assembly.