ArticleEcology and evolution2019
Gene markers for exon capture and phylogenomics in ray-finned fishes.
Article in Ecology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- An attention-based deep learning model for early detection of polyphagous shot hole borer infestations in plants.BMC plant biology · 2026Article
- Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.Systematic biology · 2023Article
- The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis.Animals : an open access journal from MDPI · 2022Article
- Population Structure, Genetic Diversity, and Conservation Strategies of a Commercially Important Sleeper Fish,Frontiers in genetics · 2022Article
- Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes).Systematic biology · 2021Article
- Article
- Mobile Elements in Ray-Finned Fish Genomes.Life (Basel, Switzerland) · 2020Review
- Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River.Ecology and evolution · 2019Article
- Gene markers for exon capture and phylogenomics in ray-finned fishes.Ecology and evolution · 2019Article
- Assexon: Assembling Exon Using Gene Capture Data.Evolutionary bioinformatics online · 2019Article
- Multilocus DNA barcoding - Species Identification with Multilocus Data.Scientific reports · 2017Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene capture coupled with the next-generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray-finned fishes. Here, we identified a suite of "single-copy" protein-coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and nine orders or higher clades: Acipenseriformes, Lepisosteiformes, Elopomorpha, Osteoglossomorpha, Clupeiformes, Cypriniformes, Gobiaria, Carangaria, and Eupercaria; sensu Betancur et al. 2013). Sorting the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic levels. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may greatly enrich the batteries of exon markers for phylogenomic study in ray-finned fishes.
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