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 t...
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2025-03-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-025-01314-5 |
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| author | Li-Yao Yang Li-Kun Huang Jin-Bin Lin Cun-Jing Xu Wei-Qi Tang Bi-Guang Huang |
| author_facet | Li-Yao Yang Li-Kun Huang Jin-Bin Lin Cun-Jing Xu Wei-Qi Tang Bi-Guang Huang |
| author_sort | Li-Yao Yang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-7cec6a150f3944f299290eeb7fd246db |
| institution | OA Journals |
| issn | 2730-6844 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
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| series | BMC Genomic Data |
| spelling | doaj-art-7cec6a150f3944f299290eeb7fd246db2025-08-20T02:10:20ZengBMCBMC Genomic Data2730-68442025-03-012611410.1186/s12863-025-01314-5Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristataLi-Yao Yang0Li-Kun Huang1Jin-Bin Lin2Cun-Jing Xu3Wei-Qi Tang4Bi-Guang Huang5College of Geography and Oceanography, Minjiang UniversityXiamen Jointgene Biotechnology Co., LtdCollege of Geography and Oceanography, Minjiang UniversityCollege of Geography and Oceanography, Minjiang UniversityCollege of Geography and Oceanography, Minjiang UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry UniversityAbstract 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.https://doi.org/10.1186/s12863-025-01314-5Hygroryza aristataHaplotype-resolvedGap-freeGenome assemblyGenome annotationPacBio HiFi |
| spellingShingle | Li-Yao Yang Li-Kun Huang Jin-Bin Lin Cun-Jing Xu Wei-Qi Tang Bi-Guang Huang Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata BMC Genomic Data Hygroryza aristata Haplotype-resolved Gap-free Genome assembly Genome annotation PacBio HiFi |
| title | Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata |
| title_full | Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata |
| title_fullStr | Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata |
| title_full_unstemmed | Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata |
| title_short | Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata |
| title_sort | haplotype resolved and gap free genome of a floating aquatic plant from the oryzeae tribe hygroryza aristata |
| topic | Hygroryza aristata Haplotype-resolved Gap-free Genome assembly Genome annotation PacBio HiFi |
| url | https://doi.org/10.1186/s12863-025-01314-5 |
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