Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Convergent evolution of cichlid vision

ABSTRACT: Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments

PROVIDER: PRJEB32048 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3264100_1.fastq.gz	Fastqsanger.gz
	ERR3264100_2.fastq.gz	Fastqsanger.gz
	ERR3264110_1.fastq.gz	Fastqsanger.gz
	ERR3264110_2.fastq.gz	Fastqsanger.gz
	ERR3264120_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 272

Similar Datasets

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

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

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 | GSE252805 | GEO

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

2024-04-01 | GSE252804 | GEO

Project description:Diversity in visual sensitivity in Neotropical cichlid fishes via differential and intraretinal variation in opsin gene expression

| PRJNA701195 | ENA

Project description:Convergent genomic basis of lip trophic novelties in cichlid fishes

| PRJNA818269 | ENA

Divergent gene expression regulation in an African cichlid

Project description:Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes

| PRJEB57348 | ENA

Gut microbiota of Midas cichlid fishes

Project description:16S rRNA amplicon sequencing of the cichlid fishes gut microbiota from Nicaraguan lakes Raw sequence reads

| PRJNA531389 | ENA

Rapid speciation of cichlids fishes may be explained by evolutionary divergence of novel open reading frames

Project description:We have investigated whether we can understand the speciation of the cichlid fishes using proteogenomic approach. We have deposited both the RNA-Seq data and Mass Spectra data here. Details of methods carried out can be found in the Methods Section of the paper.

2021-09-09 | PXD019072 | 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

Copy Number Variation across 12 tribes of African cichlid species

Project description:This study examines genomic copy-number variation among African cichlids spanning multiple tribes and radiations. We map CNVs and hotspots throughout the Oreochromis niloticus reference genome, categorize gene ontology enrichment within CNV regions, and compare results with sequence-based cichlid phylogenies.

2019-07-26 | GSE117914 | 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