Genome assembly of Rhinogobius sp. YB in Okinawa Island, Japan
Data files
May 05, 2026 version files 3.10 GB
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README.md
2.33 KB
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YB_assembly.v20231018.fa
995.88 MB
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YB_assembly.v20231018.gff
101.50 MB
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YB_assembly.v20231018.hardmasked.fa
999.14 MB
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YB_assembly.v20231018.softmasked.fa
999.14 MB
Abstract
The genus Rhinogobius comprises freshwater gobiid fishes that have diversified in East Asia and Southeast Asia. To advance genomic studies of the diversification mechanisms of Rhinogobius, we assembled a chromosome-scale genome of Rhinogobius sp. YB, a strictly freshwater species inhabiting Okinawa Island, Japan. The sample was collected with permission from the local authorities. Genomic data were generated using the following technologies: Oxford Nanopore, 10x Genomics linked-read, and Hi-C sequencing. This dataset includes the assembled genome sequence, a repeat-masked genome file, and gene annotations. This genome will be useful as a reference sequence for short-read mapping and as a resource for comparative genomic analyses.
Chromosome-scale genome assembly for a Japanese Rhinogobius species, Rhinogobius sp. YB, using Oxford Nanopore, 10x Genomics linked-read, and Hi-C sequencing technologies.
General information
Data type
- Oxford Nanopore MinION long reads (two FLO-MIN110 [R10.3] flow cells and one FLO-MIN106D [R9.4.1] flow cell) for contig assembly
- Illumina short reads for polishing the Oxford Nanopore assembly
- 10x Genomics linked reads for contig correction and scaffolding
- Hi-C data generated using the iconHi-C method for chromosome-scale scaffolding
Date of sample collection
Data were generated from three individuals. Sampling was conducted with permission from Okinawa Prefecture.
- Oxford Nanopore long reads and Illumina short reads: 2019-04-21
- 10x Genomics linked reads: 2017-08-05
- Hi-C: 2022-10-24
Geographic location of data collection
- Yofuke River, Nago City, Okinawa Prefecture, Japan
Description of the data and file structure
Files
- YB_assembly.v20231018.fa
FASTA file containing the genome assembly of Rhinogobius sp. YB. Reads from three Oxford Nanopore MinION flow cells were assembled using Flye v2.9.2. The resulting contigs were polished with Illumina short reads using Hypo v1.0.3. Haplotigs were removed with PurgeHaplotigs v1.1.2. The contigs were then corrected and scaffolded using 10x Genomics linked reads with Tigmint v1.2.9 and ARCS v1.2.5. The resulting scaffolds were further scaffolded with Hi-C reads to produce a chromosome-scale assembly using YaHS v1.2, followed by manual curation in Juicebox v1.11.08. - YB_assembly.v20231018.gff
Gene annotation file. The genome was annotated using BRAKER v3.0.7, Helixer v0.3.2, and GeMoMa v1.9. - YB_assembly.v20231018.hardmasked.fa
Hard-masked genome sequence generated using RepeatModeler v2.0.5 and RepeatMasker v4.1.2. Repetitive regions are masked with Ns. - YB_assembly.v20231018.softmasked.fa
Soft-masked genome sequence generated using RepeatModeler v2.0.5 and RepeatMasker v4.1.2. Repetitive regions are masked in lowercase letters.
Sharing and access information
License/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Related publication: Manuscript in preparation