ArticleG3 (Bethesda, Md.)2024
A high-quality reference genome for the common creek chub, Semotilus atromaculatus.
Article in G3 (Bethesda, Md.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Extensive Multi-Species Hybridization Between Leuciscidae Minnow Species.Molecular ecology · 2026Article
- T2TJournal of fungi (Basel, Switzerland) · 2026Article
- Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow (Ptychocheilus lucius).G3 (Bethesda, Md.) · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
Creek chub (Semotilus atromaculatus) is a leuciscid minnow species commonly found in anthropogenically disturbed environments, making it an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality, 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences' Improved Phase Assembly (873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1-4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic biodiversity studies of creek chub and other nonmodel leuciscid species common to disturbed environments.
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Registered trials
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