Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

PROVIDER: PRJNA552724 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9672210_1.fastq.gz	Fastqsanger.gz
	SRR9672210_2.fastq.gz	Fastqsanger.gz
	SRR9672201_1.fastq.gz	Fastqsanger.gz
	SRR9672201_2.fastq.gz	Fastqsanger.gz
	SRR9672211_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Developmental plasticity of stem cells in tooth and taste bud renewal

Project description:We use the continuously replacing dentition of Lake Malawi cichlid fishes to understand de-novo tooth replacement in adult vertebrates. In this system, each tooth is replaced in a one-for-one fashion every ~50 days. Here, we explore the source of epithelial stem cells for tooth replacement.

2019-09-23 | GSE122501 | GEO

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes [smallRNA-seq]

Project description:East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

2024-04-01 | GSE252804 | GEO

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

2024-04-01 | GSE252805 | GEO

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

Project description:East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations. While TE-derived genetic and epigenetic variability has been associated with phenotypic traits, TE expression and epigenetic silencing remain unexplored in cichlids. Here, we profiled TE expression in African cichlids, and describe dynamic expression patterns during embryogenesis and according to sex. Most TE silencing factors are conserved and expressed in cichlids. We describe an expansion of two truncated Piwil1 genes in Lake Malawi/Nyasa cichlids, encoding a Piwi domain with catalytic potential. To further dissect epigenetic silencing of TEs, we focused on small RNA-driven epigenetic silencing. We detect a small RNA population in gonads consistent with an active Piwi-interacting RNA (piRNA) pathway targeting TEs. We uncover fluid genomic origins of piRNAs in closely related cichlid species. This, along with signatures of positive selection in piRNA pathway factors, points towards fast co-evolution of TEs and the piRNA pathway. Our study is the first step to understand the contribution of ongoing TE-host arms races to the cichlid radiations in Africa.

2024-04-02 | PXD047439 | Pride

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Project description:Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.

2021-08-19 | GSE158514 | GEO

Project description:Lake Malawi haplochromine cichlid RAD

| PRJNA347810 | ENA

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Project description:Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

| PRJNA665493 | ENA

Project description:Phylogenomic analyses show repeated evolution of hypertrophied lips among Lake Malawi cichlid fishes

| PRJNA789119 | ENA

Project description:Sex chromosome evolution in cichlid fishes

| PRJNA669839 | ENA

Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish

Project description:Inheritance and plasticity of epigenetic divergence characterise early stages of speciation in an incipient cichlid species of an African crater lake.

2022-06-09 | GSE174120 | 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