title: De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes.
abstract: In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Bahar
authors.initials: B
authors.lastname: Behsaz
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada.
authors.forename: S Austin
authors.initials: SA
authors.lastname: Hammond
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Erdi
authors.initials: E
authors.lastname: Kucuk
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada.
authors.forename: Nik
authors.initials: N
authors.lastname: Veldhoen
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada.
authors.forename: Caren C
authors.initials: CC
authors.lastname: Helbing
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D007814:Larva / Q000235:genetics; D008099:Liver / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D011892:Rana catesbeiana / Q000235:genetics*; D012015:Reference Standards; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D012333:RNA, Messenger