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Front Genet
2012 Mar 14;3:37. doi: 10.3389/fgene.2012.00037.
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The metamorphosis of amphibian toxicogenomics.
Helbing CC
.
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Amphibians are important vertebrates in toxicology often representing both aquatic and terrestrial forms within the life history of the same species. Of the thousands of species, only two have substantial genomics resources: the recently published genome of the Pipid, Xenopus (Silurana) tropicalis, and transcript information (and ongoing genome sequencing project) of Xenopus laevis. However, many more species representative of regional ecological niches and life strategies are used in toxicology worldwide. Since Xenopus species diverged from the most populous frog family, the Ranidae, ~200 million years ago, there are notable differences between them and the even more distant Caudates (salamanders) and Caecilians. These differences include genome size, gene composition, and extent of polyploidization. Application of toxicogenomics to amphibians requires the mobilization of resources and expertise to develop de novo sequence assemblies and analysis strategies for a broader range of amphibian species. The present mini-review will present the advances in toxicogenomics as pertains to amphibians with particular emphasis upon the development and use of genomic techniques (inclusive of transcriptomics, proteomics, and metabolomics) and the challenges inherent therein.
Figure 1. Cartoon depiction of RNA-seq results from the liver of premetamorphic Xenopus laevis and Rana catesbeiana tadpoles focusing upon arginine and proline metabolism including the urea cycle. Tadpoles were exposed to 10 nM 3,5,3′-triiodothyronine (a thyroid hormone) or NaOH vehicle control for 48 h. The animals were treated and maintained in accordance with the guidelines of the Canadian Council on Animal Care. The liver transcriptomes were subjected to RNA-seq using 75 base HiSeq of paired end tagged (PET) libraries. The derived sequence information was assembled using the X. tropicalis genome as a scaffold and the contig identities were determined by a Blastx search against the X. tropicalis genome. The number of read counts (~400 million) was normalized between samples and the relative count frequencies of the indicated pathway components were compared based upon the X. tropicalis arginine and proline metabolism KEGG pathway (xtr00330; www.genome.jp/kegg). The results are depicted as a bipartite rectangle beside the name of the enzymes corresponding with measured transcripts in the RNA-seq experiment that were identified in the KEGG pathway. The left side represents the relative change in transcript abundance levels of Rana (R) and the right side mRNA levels of Xenopus (X) where red is increased, black is no change, and blue is decreased relative to control animals. Non-detected transcript is depicted by a crossed-out white box. Use of the X. tropicalis genome as an assembly scaffold had limited utility since X. laevis and R. catesbeiana sequences aligned imperfectly to the X. tropicalis genome with R. catesbeiana, not surprisingly, having the least benefit of alignment. Nevertheless, some transcript identities linked to count frequencies were positively confirmed and the data obtained for the urea cycle enzymes, for example, matched well with previous observations (Helbing et al., 1992; Xu et al., 1993; Iwase et al., 1995). This validates the method for transcripts that are identifiable and quantifiable in this way.
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