稻族漂浮水生植物尖叶水禾的单倍型解析且无间隙基因组。

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

作者信息

Yang Li-Yao, Huang Li-Kun, Lin Jin-Bin, Xu Cun-Jing, Tang Wei-Qi, Huang Bi-Guang

机构信息

College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China.

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.

出版信息

BMC Genom Data. 2025 Mar 28;26(1):23. doi: 10.1186/s12863-025-01314-5.

DOI:10.1186/s12863-025-01314-5

PMID:40148752

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11951829/

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.

摘要

目标

水禾是一种原产于东南亚的水生植物，对水生环境具有高度适应性。水禾属于稻族，与水稻（Oryza sativa）亲缘关系密切，在作物改良方面具有潜力，尤其是在耐洪性方面。本研究旨在对水禾的基因组进行测序和组装。

数据描述

我们使用31.91 Gb的太平洋生物科学公司（PacBio）高保真（HiFi）数据和22.36 Gb的超长牛津纳米孔技术（ONT）数据组装了水禾的基因组，得到了两个无间隙单倍型基因组，hap1（349.74 Mb）和hap2（347.98 Mb），每个基因组有12条染色体和23个端粒。染色体的连续性得到了高通量染色体构象捕获（Hi-C）数据的支持。组装结果显示出高完整性，每个单倍型的覆盖率>99.8%，基准通用单拷贝直系同源基因（BUSCO）得分98.4%，长末端重复序列组装指数（LAI）得分>11.0。为了进行基因组注释，我们生成了六个组织的RNA测序（RNA-seq）数据（176.06 Gb），分别在hap1和hap2中鉴定出39139个和38746个蛋白质编码基因。