Chromosomal-level Assembly of Tokudaia Osimensis, Tokudaia Tokunoshimensis, and Tokudaia Muenninki Genomes

Overview

Journal Sci Data

Specialty Science

Date 2023 Dec 21

PMID 38129438

Authors

Miki Okuno

Yuta Mochimaru

Kentaro Matsuoka

Takahiro Yamabe

Luisa Matiz-Ceron

Takamichi Jogahara

Atsushi Toyoda

Asato Kuroiwa

Takehiko Itoh

Affiliations

Soon will be listed here.

Abstract

Herein, we present the first high-quality long-read-based chromosome-level genome assemblies and gene annotations of the genomes of three endangered Tokudaia species: Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki. These species, which are endemic to different islands of the Ryukyu Islands, Japan, exhibited unique karyotypes and sex chromosomal characteristics. The genome assemblies generated using PacBio, Illumina, and Hi-C sequence data consisted of 13 (corresponded to 12 autosomes and one X chromosome), 23 (corresponded to 22 autosomes and one X chromosome), and 23 (corresponded to 21 autosomes and the neo- and ancestral X regions) chromosome-level scaffolds that contained 2,445, 2,477, and 2,661 Mbp of sequence data, respectively. Annotations of protein-coding genes were performed using RNA-Seq-based, homology-based, and Ab initio methods. BUSCO completeness values for every species exceeded 96% for genomes and 98% for genes. These data can be an important resource for contributing to our understanding of species genomes resulting from allopatric speciation and provide insights into mammalian sex-determination mechanisms and sex chromosome evolution.

Citing Articles

Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes.

Okuno M, Mochimaru Y, Matsuoka K, Yamabe T, Matiz-Ceron L, Jogahara T Sci Data. 2023; 10(1):927.

PMID: 38129438 PMC: 10739956. DOI: 10.1038/s41597-023-02845-1.

References

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

Zushi H, Murata C, Mizushima S, Nishida C, Kuroiwa A . Unique XCI evolution in Tokudaia: initial XCI of the neo-X chromosome in Tokudaia muenninki and function loss of XIST in Tokudaia osimensis. Chromosoma. 2017; 126(6):741-751. DOI: 10.1007/s00412-017-0639-4. View

Murata C, Yamada F, Kawauchi N, Matsuda Y, Kuroiwa A . The Y chromosome of the Okinawa spiny rat, Tokudaia muenninki, was rescued through fusion with an autosome. Chromosome Res. 2011; 20(1):111-25. DOI: 10.1007/s10577-011-9268-6. View

Rhie A, Walenz B, Koren S, Phillippy A . Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1):245. PMC: 7488777. DOI: 10.1186/s13059-020-02134-9. View

Arakawa Y, Nishida-Umehara C, Matsuda Y, Sutou S, Suzuki H . X-chromosomal localization of mammalian Y-linked genes in two XO species of the Ryukyu spiny rat. Cytogenet Genome Res. 2003; 99(1-4):303-9. DOI: 10.1159/000071608. View

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

Ranallo-Benavidez T, Jaron K, Schatz M . GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020; 11(1):1432. PMC: 7080791. DOI: 10.1038/s41467-020-14998-3. View

Wu T, Watanabe C . GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005; 21(9):1859-75. DOI: 10.1093/bioinformatics/bti310. View

Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander E, Getz G . Integrative genomics viewer. Nat Biotechnol. 2011; 29(1):24-6. PMC: 3346182. DOI: 10.1038/nbt.1754. View

10.

Guan D, McCarthy S, Wood J, Howe K, Wang Y, Durbin R . Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020; 36(9):2896-2898. PMC: 7203741. DOI: 10.1093/bioinformatics/btaa025. View

11.

Marcais G, Kingsford C . A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27(6):764-70. PMC: 3051319. DOI: 10.1093/bioinformatics/btr011. View

12.

Murata C, Kuroki Y, Imoto I, Kuroiwa A . Ancestral Y-linked genes were maintained by translocation to the X and Y chromosomes fused to an autosomal pair in the Okinawa spiny rat Tokudaia muenninki. Chromosome Res. 2016; 24(3):407-19. DOI: 10.1007/s10577-016-9531-y. View

13.

Okuno M, Mochimaru Y, Matsuoka K, Yamabe T, Matiz-Ceron L, Jogahara T . Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Sci Data. 2023; 10(1):927. PMC: 10739956. DOI: 10.1038/s41597-023-02845-1. View

14.

Dudchenko O, Batra S, Omer A, Nyquist S, Hoeger M, Durand N . De novo assembly of the genome using Hi-C yields chromosome-length scaffolds. Science. 2017; 356(6333):92-95. PMC: 5635820. DOI: 10.1126/science.aal3327. View

15.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

16.

Durand N, Shamim M, Machol I, Rao S, Huntley M, Lander E . Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016; 3(1):95-8. PMC: 5846465. DOI: 10.1016/j.cels.2016.07.002. View

17.

Jin J, Yu W, Yang J, Song Y, dePamphilis C, Yi T . GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1):241. PMC: 7488116. DOI: 10.1186/s13059-020-02154-5. View

18.

Murata C, Yamada F, Kawauchi N, Matsuda Y, Kuroiwa A . Multiple copies of SRY on the large Y chromosome of the Okinawa spiny rat, Tokudaia muenninki. Chromosome Res. 2010; 18(6):623-34. DOI: 10.1007/s10577-010-9142-y. View

19.

Kim D, Paggi J, Park C, Bennett C, Salzberg S . Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37(8):907-915. PMC: 7605509. DOI: 10.1038/s41587-019-0201-4. View

20.

Manni M, Berkeley M, Seppey M, Simao F, Zdobnov E . BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021; 38(10):4647-4654. PMC: 8476166. DOI: 10.1093/molbev/msab199. View