ArticleGenome biology and evolution2011
Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 61 citations in OpenAlex.
- Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly.Scientific reports · 2025Article
- Evolution of MHC IIB Diversity Across Cichlid Fish Radiations.Genome biology and evolution · 2023Review
- Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style.Nature communications · 2023Article
- Article
- Evolutionary divergence of novel open reading frames in cichlids speciation.Scientific reports · 2020Article
- Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes.Human genomics · 2019Article
- The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species.Genome biology and evolution · 2019Article
- Time matters! Developmental shift in gene expression between the head and the trunk region of the cichlid fish Astatotilapia burtoni.BMC genomics · 2019Article
- The puzzling phylogeography of the haplochromine cichlid fishEcology and evolution · 2018Article
- De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish.BMC genomics · 2018Article
- De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species.BMC genomics · 2018Article
- Parental investment matters for maternal and offspring immune defense in the mouthbrooding cichlid Astatotilapia burtoni.BMC evolutionary biology · 2017Article
- Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.Cell host & microbe · 2017Article
- Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes.PloS one · 2017Article
- Transcriptomic comparison of invasive bigheaded carps (Ecology and evolution · 2016Article
- Article
- Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses.Journal of virology · 2016Article
- Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).BMC genomics · 2015Article
- Evolutionary Fate of the Androgen Receptor-Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids.G3 (Bethesda, Md.) · 2015Article
- Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved.RNA (New York, N.Y.) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-phenotype processes in adaptive radiations. Here we report the functional annotation and comparative analyses of transcriptome data sets for two eastern African cichlid species, Astatotilapia burtoni and Ophthalmotilapia ventralis, representatives of the modern haplochromines and ectodines, respectively. Nearly 647,000 expressed sequence tags were assembled in more than 46,000 contigs for each species using the 454 sequencing technology, largely expanding the current sequence data set publicly available for these cichlids. Total predicted coverage of their proteome diversity is approximately 50% for both species. Comparative qualitative and quantitative analyses show very similar transcriptome data for the two species in terms of both functional annotation and relative abundance of gene ontology terms expressed. Average genetic distance between species is 1.75% when all transcript types are considered including nonannotated sequences, 1.33% for annotated sequences only including untranslated regions, and decreases to nearly half, 0.95%, for coding sequences only, suggesting a large contribution of noncoding regions to their genetic diversity. Comparative analyses across the two species, tilapia and the outgroup medaka based on an overlapping data set of 1,216 genes (∼526 kb) demonstrate cichlid-specific signature of disruptive selection and provide a set of candidate genes that are putatively under positive selection. Overall, these data sets offer the genetic platform for future comparative analyses in light of the upcoming genomes for this taxonomic group.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.