High Conopeptide Diversity in Conus tribblei Revealed Through Analysis of Venom Duct Transcriptome Using Two High-Throughput Sequencing Platforms

Abstract

The venom of each species of Conus contains different kinds of pharmacologically-active peptides which are mostly unique to that species. Collectively, the ~500 – 700 species of Conus produce a large number of these peptides, perhaps exceeding 140,000 different types in total. To date, however, only a small fraction of this diversity has been characterized via transcriptome sequencing. In addition, the sampling of this chemical diversity has not been uniform across the different lineages in the genus. In this study, we used high-throughput transcriptome sequencing approach to further investigate the diversity of Conus venom peptides. We chose a species, Conus tribblei, as a representative of a poorly studied clade of Conus. Using the Roche 454 and Illumina platforms, we discovered 136 unique and novel putative conopeptides belonging to 30 known gene superfamilies and 6 new conopeptide groups, the greatest diversity so far observed from a transcriptome. Most of the identified peptides exhibited divergence from the known conopeptides and some contained cysteine frameworks observed for the first time in cone snails. In addition, several enzymes involved in post-translational modification of conopeptides and also some proteins involved in efficient delivery of the conopeptides to prey were identified as well. Interestingly, a number of conopeptides highly similar to the conopeptides identified in a phylogenetically distant species, the generalist feeder Conus californicus, were observed. The high diversity of conopeptides and the presence of conopeptides similar to those in C. californicus suggest that C. tribblei may have a broad range of prey preferences.

Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome

“…A transcript with highly similar signal and pro regions (Fig. S1a) was previously identified in the C. tribblei transcriptome (Barghi et al 2015a). Two conopeptide genes belonging to J superfamily also lacked intron (Fig.…”

“…1). For one of these genes encoding the Ctr_45_T transcript (Barghi et al 2015a; Fig. S1b) one single exon encompassed 234 bp of the coding sequence of the whole precursor, 24 bp of 5′ UTR, and 19 bp of 3′ UTR.…”

An efficient transcriptome analysis pipeline to accelerate venom peptide discovery and characterisation

“…Using only these scores as a guide to delineate new superfamilies can lead to cases where sequences are misclassified as seen for the Coninsulins that were incorrectly classified as new superfamilies in two different studies Lavergne et al, 2013). In addition, while the majority of conotoxins are small disulfide-rich peptides and thus easily detected, larger sequences such as con-ikot-ikots that have widely varying signal regions (Barghi et al, 2014) maybe missed as seen in our reanalysis of the C. miles transcriptome. The pipeline described here integrates ConoSorter with a series of freely available bioinformatics tools in an eliminatory workflow before similarity searching to accelerate toxin discovery and classification.…”

“…combined with the much greater sequencing depth provided by the platform (Schirmer et al, 2015) has already started to be used to sequence venom gland transcriptomes producing much larger datasets (Barghi et al, 2015;Lavergne et al, 2015).…”

“…While our reanalyses have been performed on 454 pyrosequencing data, which has been the most commonly used platform for the analysis of cone snail venom gland transcriptomes thus far (Prashanth et al, 2014), more recent studies (Barghi et al, 2015;Lavergne et al, 2015) have begun to use Illumina sequencing technology (Schirmer et al, 2015), generating shorter reads but more data and uncovering further sequence diversity (Lavergne et al, 2015). Since ConoSorter is able to handle these larger datasets after assembly (Lavergne et al, 2015), it follows that our pipeline is well placed to probe larger datasets.…”