Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide RNA-seq]

ABSTRACT: The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide RNA-seq]

PROVIDER: PRJNA1187226 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31371106_1.fastq.gz	Fastqsanger.gz
	SRR31371106_2.fastq.gz	Fastqsanger.gz
	SRR31371107_1.fastq.gz	Fastqsanger.gz
	SRR31371107_2.fastq.gz	Fastqsanger.gz
	SRR31371108_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide DNA-seq]

Project description:Koala Retrovirus-A is a gamma-retrovirus sweeping wild koalas via a combination of horizontal and vertical transfer, contributing substantial genomic diversity across and even within koala populations. While studies have estimated KoRV-A's integration into the koala genome occurred 120–50,000 years ago, the origin and spread patterns of its endogenization remain unclear. Here, we analyze KoRV-A germline insertions using whole-genome sequencing data from 405 wild koalas, encompassing nearly the full koala habitat range. We map a trajectory of KoRV-A evolution and propose that KoRV-A first entered the koala germline genome near Coffs Harbour. As KoRV-A spread, replication-competitive subtypes emerged, two of which recombined with an ancient endogenous retrovirus, PhER, resulting in distinct recombination variants across northern and southern koala populations. Additionally, we identified a geographic barrier north of Sydney, which has slowed the southward spread of KoRV-A into Sydney and beyond.

2025-01-15 | GSE282117 | GEO

The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide RNA-seq]

2025-01-15 | GSE282118 | GEO

The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide DNA-seq]

Project description:The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide DNA-seq]

| PRJNA1187227 | ENA

Adaptive evolution of KoRV-A retroviral silencing in wild koalas [DNA-seq]

Project description:Koala Retrovirus-A is spreading through wild koalas in a north to south wave while transducing the germline, generating heritable genetic modifications as it transitions to an endogenous retrovirus. In animals south of Brisbane, we previously found that KoRV-A is expressed in the germline, but the resulting unspliced genomic transcripts are processed into sense strand piRNAs, post-transcriptionally suppressing replication. Here we show that this initial “innate” response is prevalent in animals south of the Brisbane River, but KoRV-A promoters are methylated and the virus is transcriptionally silenced in a subpopulation of animals north of the river. Transcriptional silencing correlates with capture of an anti-sense KoRV-A provirus by the 3’UTR of the MAP4K4 gene. The resulting hybrid transcripts are processed into anti-sense piRNAs, which transcriptionally silence established endogenous retroviruses in the germline. This provirus is sweeping through northern koalas, supporting a direct role in adaptive evolution of KoRV-A transcriptional silencing.

2025-01-15 | GSE276618 | GEO

Adaptive evolution of KoRV-A retroviral silencing in wild koalas [RNA-seq]

2025-01-15 | GSE276616 | GEO

Adaptive evolution of KoRV-A retroviral silencing in wild koalas [small RNA-seq]

2025-02-20 | GSE276617 | GEO

Centromeric chromatin in Koala

Project description:We report high throughput sequencing of DNA associated with centromeric chromatin in the koala genome.

2018-04-26 | GSE111153 | GEO

Antibody response against koala retrovirus (KoRV) in koalas harboring KoRV-A in the presence or absence of KoRV-B.

Project description:Koala retrovirus (KoRV) is in the process of endogenization into the koala (Phascolarctos cinereus) genome and is currently spreading through the Australian koala population. Understanding how the koala's immune system responds to KoRV infection is critical for developing an efficacious vaccine to protect koalas. To this end, we analyzed the antibody response of 235 wild koalas, sampled longitudinally over a four-year period, that harbored KoRV-A, and with or without KoRV-B. We found that the majority of the sampled koalas were able to make anti-KoRV antibodies, and that there was a linear increase in anti-KoRV IgG levels in koalas up to approximately seven years of age and then a gradual decrease thereafter. Koalas infected with both KoRV-A and KoRV-B were found to have slightly higher anti-KoRV IgG titers than koalas with KoRV-A alone and there was an inverse relationship between anti-KoRV IgG levels and circulating KoRV viral load. Finally, we identified distinct epitopes on the KoRV envelope protein that were recognized by antibodies. Together, these findings provide insight into the koala's immune response to KoRV and may be useful in the development of a therapeutic KoRV vaccine.

| S-EPMC6711960 | biostudies-literature

Proteomic analysis of koala (Phascolarctos cinereus) spermatozoa and prostatic bodies

Project description:The aims of this study were to investigate the proteome of koala (Phascolarctos cinereus) spermatozoa and that of the prostatic bodies with which they form intimate contact at the moment of ejaculation. For this purpose, spermatozoa and prostatic bodies were obtained from four adult male koala by electroejaculation and analysed by high performance liquid chromatography coupled to a mass spectrometer. This strategy successfully identified and 744 koala sperm and 1,297 prostatic body proteins, which were subsequently attributed to 482 and 776 unique gene products, respectively. Gene ontology curation of the koala sperm proteome revealed an abundance of proteins mapping to the canonical sirtuin and 14-3-3 signalling pathways. By contrast, protein ubiquitination and unfolding protein response pathways dominated the equivalent analysis of proteins uniquely identified in koala prostatic bodies. In terms of functional annotation, koala sperm proteins commonly mapped to the categories of cellular compromise/inflammatory response, whilst those of the prostatic body revealed an over-representation of molecular chaperone and stress-related proteins associated with cell survival. Cross-species comparisons demonstrated that the koala sperm proteome displays greater conservation with that of eutherians (human; 93%) as opposed to reptile (crocodile; 39%) and avian (rooster; 27%) spermatozoa. Similarly, koala prostatic body proteins also presented a relatively high degree of overlap (70%) with those identified in sub-populations of large human seminal plasma extracellular vesicles. Together, this work contributes our overall understanding of the core sperm proteome and has identified candidate markers that may contribute to the exceptional longevity of koala spermatozoa during ex vivo storage.

2021-08-23 | PXD024250 | Pride

Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

Project description:We examined genome-wide patterns of DNA methylation from whole genome DNA methylation maps of five tissues (brain, kidney, lung, skeletal muscle, and pancreas) from one male koala and one female koala (Phascolarctos cinereus), and present the first whole genome, multi-tissue “methylome atlas” with information on tissue- and sex-specific variation of DNA methylation for a marsupial.

2021-02-27 | GSE149600 | GEO

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