Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tokudaia osimensis osimensis

ABSTRACT: Hi-C seq and RNA-seq in species, genus Tokudaia

PROVIDER: PRJDB14616 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR426688_1.fastq.gz	Fastqsanger.gz
	DRR426688_2.fastq.gz	Fastqsanger.gz
	DRR426689_1.fastq.gz	Fastqsanger.gz
	DRR426689_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Tokudaia osimensis

Project description:Tokudaia osimensis overview

| PRJNA895513 | ENA

Tokudaia osimensis

Project description:Tokudaia osimensis Transcriptome or Gene expression

| PRJNA474959 | ENA

Tokudaia osimensis

Project description:Whole genome sequences of the Amami spiny rat, Tokudaia osimensis

| PRJDB5072 | ENA

Tokudaia osimensis

Project description:Alternate Pseudohaplotype genome sequences of the Amami spiny rat, Tokudaia osimensis

| PRJDB16414 | ENA

Tokudaia osimensis

Project description:Principal pseudohaplotype genome sequences of the Amami spiny rat, Tokudaia osimensis

| PRJDB16491 | ENA

Tokudaia osimensis

Project description:Comparison of the genome sequences between sexes in the Amami spiny rat, Tokudaia osimensis

| PRJDB12028 | ENA

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.

| S-EPMC10739956 | biostudies-literature

Tokudaia muenninki

Project description:Tokudaia muenninki overview

| PRJNA448473 | ENA

Tokudaia tokunoshimensis

Project description:Tokudaia tokunoshimensis overview

| PRJNA1014547 | ENA

Molecular mechanism of male differentiation is conserved in the SRY-absent mammal, Tokudaia osimensis.

Project description:The sex-determining gene SRY induces SOX9 expression in the testes of eutherian mammals via two pathways. SRY binds to testis-specific enhancer of Sox9 (TESCO) with SF1 to activate SOX9 transcription. SRY also up-regulates ER71 expression, and ER71 activates Sox9 transcription. After the initiation of testis differentiation, SOX9 enhances Amh expression by binding to its promoter with SF1. SOX8, SOX9 and SOX10, members of the SOXE gene family, also enhance the activities of the Amh promoter and TESCO. In this study, we investigated the regulation of these sexual differentiation genes in Tokudaia osimensis, which lacks a Y chromosome and the SRY gene. The activity of the AMH promoter was stimulated by SOXE genes and SF1. Mutant AMH promoters, with mutations in its SOX and SF1 binding sites, did not show significant activity by SOX9 and SF1. These results indicate that AMH expression was regulated by the binding of SOX9 and SF1. By contrast, SOXE genes could not enhance TESCO activity. These results indicate that TESCO enhancer activity was lost in this species. Furthermore, the activity of the SOX9 promoter was enhanced by ER71, indicating that ER71 may play an important role in the testis-specific expression of SOX9.

| S-EPMC5017195 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data