ArticleMolecular biology and evolution2016
An Exon-Capture System for the Entire Class Ophiuroidea.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Article
- Article
- VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes.Molecular ecology resources · 2024Article
- Genetic variation in the brooding brittle-star: a global hybrid polyploid complex?Royal Society open science · 2024Article
- Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.Molecular ecology resources · 2022Article
- DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy.PloS one · 2022Article
- Evolutionary innovations in Antarctic brittle stars linked to glacial refugia.Ecology and evolution · 2021Article
- Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture.G3 (Bethesda, Md.) · 2021Article
- Relict from the Jurassic: new family of brittle-stars from a New Caledonian seamount.Proceedings. Biological sciences · 2021Article
- Article
- Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα.Genome biology and evolution · 2020Article
- Mimicry and mitonuclear discordance in nudibranchs: New insights from exon capture phylogenomics.Ecology and evolution · 2020Article
- Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia).Molecular ecology resources · 2020Article
- Article
- Gene markers for exon capture and phylogenomics in ray-finned fishes.Ecology and evolution · 2019Article
- Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.Nature biotechnology · 2019Article
- Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors.Nature · 2019Article
- Assexon: Assembling Exon Using Gene Capture Data.Evolutionary bioinformatics online · 2019Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exon-capture studies have typically been restricted to relatively shallow phylogenetic scales due primarily to hybridization constraints. Here, we present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures approximately 90% of the 1,552 exon target, across all major lineages of the quarter-billion-year-old extant crown group. Key features of our system are 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map, or align; 2) use of multiple artificial representatives based on ancestral state reconstructions rather than exemplars to improve capture and mapping of the target; 3) mapping reads to a multi-reference alignment; and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences, and sample contamination. The resulting data give a well-resolved tree (currently standing at 417 samples, 275,352 sites, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.
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