A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo
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 geno...
Published in: | Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |
---|---|
Main Authors: | , , , , , |
Other Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2014
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1002/jez.b.22589 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjez.b.22589 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.22589 |
id |
crwiley:10.1002/jez.b.22589 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1002/jez.b.22589 2024-09-15T18:12:41+00:00 A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo Braasch, Ingo Peterson, Samuel M. Desvignes, Thomas McCluskey, Braedan M. Batzel, Peter Postlethwait, John H. VolkswagenStiftung, Initiative Evolutionary Biology NIH 2014 http://dx.doi.org/10.1002/jez.b.22589 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjez.b.22589 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.22589 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Journal of Experimental Zoology Part B: Molecular and Developmental Evolution volume 324, issue 4, page 316-341 ISSN 1552-5007 1552-5015 journal-article 2014 crwiley https://doi.org/10.1002/jez.b.22589 2024-09-03T04:25:30Z 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. Article in Journal/Newspaper Icefish Wiley Online Library Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 324 4 316 341 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
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. |
author2 |
VolkswagenStiftung, Initiative Evolutionary Biology NIH |
format |
Article in Journal/Newspaper |
author |
Braasch, Ingo Peterson, Samuel M. Desvignes, Thomas McCluskey, Braedan M. Batzel, Peter Postlethwait, John H. |
spellingShingle |
Braasch, Ingo Peterson, Samuel M. Desvignes, Thomas McCluskey, Braedan M. Batzel, Peter Postlethwait, John H. A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
author_facet |
Braasch, Ingo Peterson, Samuel M. Desvignes, Thomas McCluskey, Braedan M. Batzel, Peter Postlethwait, John H. |
author_sort |
Braasch, Ingo |
title |
A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
title_short |
A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
title_full |
A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
title_fullStr |
A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
title_full_unstemmed |
A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo |
title_sort |
new model army: emerging fish models to study the genomics of vertebrate evo‐devo |
publisher |
Wiley |
publishDate |
2014 |
url |
http://dx.doi.org/10.1002/jez.b.22589 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjez.b.22589 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.22589 |
genre |
Icefish |
genre_facet |
Icefish |
op_source |
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution volume 324, issue 4, page 316-341 ISSN 1552-5007 1552-5015 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/jez.b.22589 |
container_title |
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |
container_volume |
324 |
container_issue |
4 |
container_start_page |
316 |
op_container_end_page |
341 |
_version_ |
1810450281750593536 |