Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typical...

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Bibliographic Details
Published in:PloS one 2014-12, Vol.9 (12), p.e74132-e74132
Main Authors: Pereira, Joana, Johnson, Warren E, O'Brien, Stephen J, Jarvis, Erich D, Zhang, Guojie, Gilbert, M Thomas P, Vasconcelos, Vitor, Antunes, Agostinho
Format: Article
Language:English
Subjects:
Animals
Automation
Binding Sites
Bioinformatics
Biological evolution
Biology
Biology and Life Sciences
Birds
Catalysis
Cell cycle
Cholesterol
Deserts
Endoplasmic reticulum
Evolution
Evolution & development
Evolution, Molecular
Evolutionary genetics
Gene Duplication
Gene sequencing
Genomes
Genomics
Genomics - methods
Hedgehog genes
Hedgehog protein
Hedgehog Proteins - chemistry
Hedgehog Proteins - genetics
Interdisciplinary aspects
Invertebrates
Models, Molecular
Multigene Family
Neurosciences
Peptides
Phylogeny
Positive selection
Poultry - genetics
Protein Structure, Tertiary
Proteins
Reptiles - genetics
Sterols
Vertebrates
Vertebrates - genetics
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Summary:The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog--Shh; Indian hedgehog--Ihh; and Desert hedgehog--Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0074132