Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

• Published in: BMC genomics Vol. 12; no. 1; p. 259
• Main Authors: Durban, Jordi, Juárez, Paula, Angulo, Yamileth, Lomonte, Bruno, Flores-Diaz, Marietta, Alape-Girón, Alberto, Sasa, Mahmood, Sanz, Libia, Gutiérrez, José M, Dopazo, Joaquín, Conesa, Ana, Calvete, Juan J
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23.05.2011; BioMed Central; BMC
• Subjects: 454 pyrosequencing; Animals; Atropoides; bioinformatic analysis; Bothriechis; Bothrops asper; Cerrophidion; Costa Rica; Costa Rican snakes; Crotalus; DNA sequencing; Gene Expression Profiling - methods; High-Throughput Nucleotide Sequencing - methods; next generation high-throughput DNA sequencing; Nucleotide sequencing; Physiological aspects; Proteome - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Salivary Glands - metabolism; Sequence Analysis, DNA - methods; Snake venom gland transcriptomics; Snake Venoms - genetics; Snakes - classification; Snakes - genetics; Snakes - metabolism; Costa Rica; Spain
• DOI: 10.1186/1471-2164-12-259
• ISSN: 1471-2164

A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis) of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27%) were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements) and class II (DNA transposons) mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large divergence between A. mexicanus and A. picadoi, and a closer kinship between A. mexicanus and C. godmani. Our comparative next-generation sequencing (NGS) analysis reveals taxon-specific trends governing the formulation of the venom arsenal. Knowledge of the venom proteome provides hints on the translation efficiency of toxin-coding transcripts, contributing thereby to a more accurate interpretation of the transcriptome. The application of NGS to the analysis of snake venom transcriptomes, may represent the tool for opening the door to systems venomics.