Biology Faculty Articles
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 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 theHh 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 Hhparalogous 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.
Portuguese Foundation for Science and Technology grant #: CIIMAR/C2008/BII/01-25; Russian Ministry of Science grant #: 11.G34.31.0068; FCT project #s: PEst-C/MAR/LA0015/2013, PTDC/BIA-BDE/69144/2006 (FCOMP-01-0124-FEDER-007065), PTDC/AACAMB/104983/2008 (FCOMP-01-0124-FEDER-008610), PTDC/AAC-AMB/121301/2010 (FCOMP-01-0124-FEDER-019490).
Pereira, Joana; Warren E. Johnson; Stephen J. O'Brien; Erich D. Jarvis; Guojie Zhang; M. Thomas P. Gilbert; Vitor Vasconcelos; and Agostinho Antunes. 2014. "Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates." PLoS ONE 9, (12 e74132): 1-35. https://nsuworks.nova.edu/cnso_bio_facarticles/749
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©2014 Pereira et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.