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Hydrobiologia

, Volume 825, Issue 1, pp 159–175 | Cite as

Phylogenetic annotation and genomic architecture of opsin genes in Crustacea

  • Jorge L. Pérez-Moreno
  • Danielle M. DeLeo
  • Ferran Palero
  • Heather D. Bracken-Grissom
CRUSTACEAN GENOMICS

Abstract

A major goal of evolutionary biology is to understand the role of adaptive processes on sensory systems. Visual capabilities are strongly influenced by environmental and ecological conditions, and the evolutionary advantages of vision are manifest by its complexity and ubiquity throughout Metazoa. Crustaceans occupy a vast array of habitats and ecological niches, and are thus ideal taxa to investigate the evolution of visual systems. A comparative approach is taken here for efficient identification and classification of opsin genes, photoreceptive pigment proteins involved in color vision, focusing on two crustacean model organisms: Hyalella azteca and Daphnia pulex. Transcriptomes of both species were assembled de novo to elucidate the diversity and function of expressed opsins within a robust phylogenetic context. For this purpose, we developed a modified version of the Phylogenetically Informed Annotation tool’s pipeline to filter and identify visual genes from transcriptomes in a scalable and efficient manner. In addition, reference genomes of these species were used to validate our pipeline while characterizing the genomic architecture of the opsin genes. Next-generation sequencing and phylogenetics provide future venues for the study of sensory systems, adaptation, and evolution in model and nonmodel organisms.

Keywords

Evolution Phototransduction Protein RNAseq Transcriptomics Vision 

Notes

Acknowledgements

The authors would like to thank Megan Porter for access to her compilation of reference opsin data, Daniel Speiser and Todd Oakley for allowing us to modify the original PIA tool, and Katherine Dougan for advice during the preparation of this manuscript. JPM was supported by the Philip M. Smith Graduate Research Grant for Cave and Karst Research from the Cave Research Foundation, The Crustacean Society Scholarship in Graduate Studies, and Florida International University’s Dissertation Year Fellowship. This work was partially funded by two grants awarded from the National Science Foundation: Doctoral Dissertation Improvement Grant (#1701835) awarded to JPM and HBG, and the Division of Environmental Biology Bioluminescence and Vision grant (DEB-1556059) awarded to HBG. FP acknowledges project CHALLENGEN (CTM2013-48163) of the Spanish Government and a postdoctoral contract funded by the Beatriu de Pinos Programme of the Generalitat de Catalunya (2014-BPB-00038). The authors would like to thank the Instructional & Research Computing Center (IRCC) at Florida International University for providing High-Performance Computing resources that have contributed to the research results reported within this article. This is contribution #92 of the Marine Education and Research Center of the Institute for the Water and the Environment at the Florida International University.

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biological SciencesFlorida International University – Biscayne Bay CampusNorth MiamiUSA
  2. 2.Centre d’Estudis Avançats de Blanes (CEAB-CSIC)BlanesSpain

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