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Tokudaia muenninki

ABSTRACT: Transcriptome analysis isolated from fibroblast cells of Tokduaia muenninki

PROVIDER: PRJDB4734 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR059296_1.fastq.gz	Fastqsanger.gz
	DRR059296_2.fastq.gz	Fastqsanger.gz
	DRR059297_1.fastq.gz	Fastqsanger.gz
	DRR059297_2.fastq.gz	Fastqsanger.gz
	DRR059298_1.fastq.gz	Fastqsanger.gz

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Tokudaia muenninki

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Project description:Whole genome sequences of the Okinawa island spiny rat, Tokudaia muenninki

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Project description:Principal pseudohaplotype genome sequences of the Okinawa island spiny rat, Tokudaia muenninki

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Project description:Alternate pseudohaplotype genome sequences of the Okinawa island spiny rat, Tokudaia muenninki

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

Project description: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.

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Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki.

Project description:BackgroundSex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent origin in Tokudaia muenninki are expected to be evolutionarily 'young', and therefore provide a good model in which to elucidate the early phases of eutherian sex chromosome evolution. Here we describe the genomic evolution of T. muenninki in neo-sex chromosome differentiation.ResultsFISH mapping of a T. muenninki male, using 50 BAC clones as probes, revealed no chromosomal rearrangements between the neo-sex chromosomes. Substitution-direction analysis disclosed that sequence evolution toward GC-richness, which positively correlates with recombination activity, occurred in the peritelomeric regions, but not middle regions of the neo-sex chromosomes. In contrast, the sequence evolution toward AT-richness was observed in those pericentromeric regions. Furthermore, we showed genetic differentiation between the pericentromeric regions as well as an accelerated rate of evolution in the neo-Y region through the detection of male-specific substitutions by gene sequencing in multiple males and females, and each neo-sex-derived BAC sequencing.ConclusionsOur results suggest that recombination has been suppressed in the pericentromeric region of neo-sex chromosomes without chromosome rearrangement, whereas high levels of recombination activity is limited in the peritelomeric region of almost undifferentiated neo-sex chromosomes. We conclude that PAR might have been formed on the peritelomeric region of sex chromosomes as an independent event from spread of recombination suppression during the early stages of sex chromosome differentiation.

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Project description:Tokudaia osimensis Transcriptome or Gene expression

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Transcriptome analysis of fibroblast subpopulations isolated from neonatal murine dermis.

Project description:Transcriptome analysis of fibroblast subpopulations isolated from neonatal murine dermis.

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Project description:Isolated cardiomyocyte and cardiac fibroblast expression analysis

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