Anna E Savage1, Karen M Kiemnec-Tyburczy2, Amy R Ellison3, Robert C Fleischer4, Kelly R Zamudio5. 1. Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States; Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States. Electronic address: savagea@si.edu. 2. Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States. Electronic address: kmk877@humboldt.edu. 3. Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States. Electronic address: are35@cornell.edu. 4. Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States. Electronic address: fleischerr@si.edu. 5. Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States. Electronic address: kelly.zamudio@cornell.edu.
Abstract
BACKGROUND: Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts. RESULTS: To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system. CONCLUSIONS: The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.
BACKGROUND: Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts. RESULTS: To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system. CONCLUSIONS: The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.
Authors: Trenton W J Garner; Benedikt R Schmidt; An Martel; Frank Pasmans; Erin Muths; Andrew A Cunningham; Che Weldon; Matthew C Fisher; Jaime Bosch Journal: Philos Trans R Soc Lond B Biol Sci Date: 2016-12-05 Impact factor: 6.237
Authors: Stephen J Price; Trenton W J Garner; Francois Balloux; Chris Ruis; Konrad H Paszkiewicz; Karen Moore; Amber G F Griffiths Journal: PLoS One Date: 2015-06-25 Impact factor: 3.240
Authors: Francisco Pina-Martins; Bruno M Vieira; Sofia G Seabra; Dora Batista; Octávio S Paulo Journal: BMC Bioinformatics Date: 2016-01-19 Impact factor: 3.169
Authors: Eria A Rebollar; Rachael E Antwis; Matthew H Becker; Lisa K Belden; Molly C Bletz; Robert M Brucker; Xavier A Harrison; Myra C Hughey; Jordan G Kueneman; Andrew H Loudon; Valerie McKenzie; Daniel Medina; Kevin P C Minbiole; Louise A Rollins-Smith; Jenifer B Walke; Sophie Weiss; Douglas C Woodhams; Reid N Harris Journal: Front Microbiol Date: 2016-02-02 Impact factor: 5.640