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Cited by 122Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsDevelopmental Biology and Gene Regulation

A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo.

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Braasch, Ingo, Peterson, Samuel M., Desvignes, Thomas, McCluskey, Braedan M., Batzel, Peter, Postlethwait, John H.·2015·Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
DOI 10.1002/jez.b.22589PMC PMC4324401
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Abstract

Many fields of biology—including vertebrate Evo‐Devo research—are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this “genomic tsunami.” Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome‐level genome assemblies—for which we introduce the term “chromonome”—should be a key component of genomic investigations in fish because they enable large‐scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish‐related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo‐Devo research enters the postgenomic era. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 316–341, 2015 . © 2014 Wiley Periodicals, Inc.

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  • The Danioninae are an emerging model clade in the field of evo-devo, favoured for analyses of anatomy, pigmentation, gene family expansion and phylogeography.

    “The Danioninae are an emerging model clade in the field of evo-devo, favoured for analyses of anatomy (especially bone morphology and growth), pigmentation, gene family expansion and phylogeography ( Braasch et al., 2015; Parichy, 2015).”

    From The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009) (2024) · cites this paper as Braasch et al., 2015

    Section 3.3 describes danionins as an Evo-Devo model species complex and identifies variation in craniofacial anatomy, size, mineralization, and pigmentation as reasons to study them. It does not identify gene-family expansion or phylogeography as particular strengths of danionins; its discussion of genome duplication concerns another cyprinid subfamily, Cyprininae. Page numbers are unavailable in our copy. (LLM, conf=0.87)

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Authors
Braasch, I., Peterson, S. M., Desvignes, T., McCluskey, B. M., Batzel, P., & Postlethwait, J. H.
Affiliations
University of Oregon (US)
Corresponding author
  • Braasch, Ingo
  • Postlethwait, John H.
ORCID
Venue
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
Publisher
Wiley
Published
2014-08-11
Volume
324
Issue
4
Pages
316-341
ISSN
  • 1552-5007 (ISSN-L)
  • 1552-5015
DOI
10.1002/jez.b.22589
PMC
PMC4324401
OpenAlex
W1545644237
Cited by
122
References
5
Citations by year
2026: 6 · 2025: 8 · 2024: 5 · 2023: 9 · 2022: 7 · 2021: 12 · 2020: 11 · 2019: 12 · 2018: 10 · 2017: 12 · 2016: 16 · 2015: 12 · 2014: 2
FWCI
1.33
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • Journal of Experimental Zoology Part B Molecular and Developmental Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • VolkswagenStiftung, Initiative Evolutionary Biology (I/84 815)
  • NIH (R01OD011116, R01AG031922, R24OD011199, R24RR032670)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
fish genomics, vertebrate evolution, chromosome-level genome assembly, conserved synteny, teleost genome duplication, spotted gar, zebrafish, medaka, cavefish, Poeciliidae, icefish, Cyprinidae, genetic instruments, model organisms, evolutionary genomics
MeSH terms
Animals, Fishes, Phylogeny, Genome, Evolution, Molecular, Genomics, Models, Animal, Synteny, High-Throughput Nucleotide Sequencing, Transcriptome

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