De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate

Abstract

Amphibians are highly vulnerable and diverse vertebrates for which we still have modest genomic resources. Amphibian larvae are key components of continental wetlands, where they have strong influences on energy fluxes, nutrient cycling, and community structure. Amphibian larvae are highly sensitive to environmental conditions and can often alter their physiology, behavior and even morphology in response to the local conditions experienced, although we still know relatively little about the transcriptomic changes that enable such plasticity. Here we contribute the larval transcriptomes of two spadefoot toad species with divergent developmental rates and degree of developmental plasticity in response to pond drying.

Keywords: Amphibian development; amphibian transcriptomes; cross-species comparisons; developmental plasticity; developmental rate.

Figure 1

Number of transcripts (using grouped highest scoring segment pairs) per alignment coverage bins when querying against the SwissProt and Xenpus tropicalis proteome sequence databases.

Figure 2

PANTHER functional classification of transcriptomes. Wedge size reflect number of unique genes per category and out/in, black/red arrow annotations specify significant over/under representation of the GO-slim term compared to the X. tropicalis reference database.

Figure 3

gProfiler gene pathway enrichment showing symmetrical Manhattan plots of annotated terms and gene pathways for P. cultripes (above) and S. couchii (below). Color code reflects annotation domains (Gene Ontology - Biological Processes, KEGG and Reactome gene pathways) with darker shading highlighting overrepresented terms (adj. P < 0.05). Term size reflects mean expression (TPM) and overrepresented terms that are unique to each species are outlined in gray and labeled.

Figure 4

OrthoFinder results showing a) the percentage of genes that could be assigned to orthogroups per species (darker shading represents percentage of genes in species-specific orthogroups) and b) the number of species-specific and shared orthogroups recovered.