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Comp Biochem Physiol C Toxicol Pharmacol. 2014 Jun;163:24-36. doi: 10.1016/j.cbpc.2014.01.005. Epub 2014 Jan 30.

Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods.

Author information

1
Institute of Neuroscience, University of Oregon, Eugene, 97403-1254 OR, USA. Electronic address: ibraasch@uoneuro.uoregon.edu.
2
INRA, UR1037 LPGP, Campus de Beaulieu, F-35000 Rennes, France. Electronic address: yann.guiguen@rennes.inra.fr.
3
Institute of Neuroscience, University of Oregon, Eugene, 97403-1254 OR, USA. Electronic address: loker@uoregon.edu.
4
Institute of Neuroscience, University of Oregon, Eugene, 97403-1254 OR, USA. Electronic address: letaw@ohsu.edu.
5
Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA. Electronic address: allyse.ferrara@nicholls.edu.
6
INRA, UR1037 LPGP, Campus de Beaulieu, F-35000 Rennes, France. Electronic address: Julien.Bobe@rennes.inra.fr.
7
Institute of Neuroscience, University of Oregon, Eugene, 97403-1254 OR, USA. Electronic address: jpostle@uoneuro.uoregon.edu.

Abstract

Teleost fish are important models for human biology, health, and disease. Because genome duplication in a teleost ancestor (TGD) impacts the evolution of teleost genome structure and gene repertoires, we must discriminate gene functions that are shared and ancestral from those that are lineage-specific in teleosts or tetrapods to accurately apply inferences from teleost disease models to human health. Generalizations must account both for the TGD and for divergent evolution between teleosts and tetrapods after the likely two rounds of genome duplication shared by all vertebrates. Progress in sequencing techniques provides new opportunities to generate genomic and transcriptomic information from a broad range of phylogenetically informative taxa that facilitate detailed understanding of gene family and gene function evolution. We illustrate here the use of new sequence resources from spotted gar (Lepisosteus oculatus), a rayfin fish that diverged from teleosts before the TGD, as well as RNA-Seq data from gar and multiple teleost lineages to reconstruct the evolution of the Paired-related homeobox (Prrx) transcription factor gene family, which is involved in the development of mesoderm and neural crest-derived mesenchyme. We show that for Prrx genes, the spotted gar genome and gene expression patterns mimic mammals better than teleosts do. Analyses force the seemingly paradoxical conclusion that regulatory mechanisms for the limb expression domains of Prrx genes existed before the evolution of paired appendages. Detailed evolutionary analyses like those reported here are required to identify fish species most similar to the human genome to optimally connect fish models to human gene functions in health and disease.

KEYWORDS:

Craniofacial; Fin/limb bud; Genome duplication; Ohnolog; Paired appendages; Prrx1; Prrx2; RNA-Seq

PMID:
24486528
PMCID:
PMC4032612
DOI:
10.1016/j.cbpc.2014.01.005
[Indexed for MEDLINE]
Free PMC Article
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