Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy

BMC Genomics

Research Article

Vincent P. Richards¹  Angela Early²  Steve M. Bogdanowicz²  Michael J. Stanhope³  Paulina D. Pavinski Bitar³  Nicholas J. Marra⁴  Mahmood S. Shivji⁵ 

[1] Department of Biological Sciences, Clemson University, 29634, Clemson, SC, USA;Department of Ecology and Evolutionary Biology, Cornell University, 14853, Ithaca, NY, USA;Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, 14853, Ithaca, NY, USA;Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, 14853, Ithaca, NY, USA;Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, 33004, Dania Beach, FL, USA;Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, 33004, Dania Beach, FL, USA;

关键词: Regional endothermy;    Adaptive immunity;    Gene ontology;    Positive selection;    RNA-seq;    Elasmobranchs;   

DOI  :  10.1186/s12864-016-3411-x

 received in 2016-03-29, accepted in 2016-12-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundComparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy.ResultsAcross seven species, we identified an average of 10,877 Swiss-Prot annotated genes from an average of 32,474 open reading frames within each species’ heart transcriptome. About half of these genes were shared between all species while the remainder included functional differences between our groups of interest (elasmobranch vs. teleost and endotherms vs. ectotherms) as revealed by Gene Ontology (GO) and selection analyses. A repeatedly represented functional category, in both the uniquely expressed elasmobranch genes (total of 259) and the elasmobranch GO enrichment results, involved antibody-mediated immunity, either in the recruitment of immune cells (Fc receptors) or in antigen presentation, including such terms as “antigen processing and presentation of exogenous peptide antigen via MHC class II”, and such genes as MHC class II, HLA-DPB1. Molecular adaptation analyses identified three genes in elasmobranchs with a history of positive selection, including legumain (LGMN), a gene with roles in both innate and adaptive immunity including producing antigens for presentation by MHC class II. Comparisons between the endothermic and ectothermic species revealed an enrichment of GO terms associated with cardiac muscle contraction in endotherms, with 19 genes expressed solely in endotherms, several of which have significant roles in lipid and fat metabolism.ConclusionsThis collective comparative evidence provides the first multi-taxa transcriptomic-based perspective on differences between elasmobranchs and teleosts, and suggests various unique features associated with the adaptive immune system of elasmobranchs, pointing in particular to the potential importance of MHC Class II. This in turn suggests that expanded comparative work involving additional tissues, as well as genome sequencing of multiple elasmobranch species would be productive in elucidating the regulatory and genome architectural hallmarks of elasmobranchs.

【 授权许可】

CC BY   
© The Author(s). 2017