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Comparative transcriptomics of the venoms of continental and insular radiations of West African cones

Citation

Abalde, Samuel; Tenorio, Manuel J.; Afonso, Carlos M. L.; Zardoya, Rafael (2020), Comparative transcriptomics of the venoms of continental and insular radiations of West African cones, Dryad, Dataset, https://doi.org/10.5061/dryad.3n5tb2rdm

Abstract

The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species and the phylogenetical signal was totally eroded at the genus level (no sequence was identified as shared-derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2, and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus. Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.

Methods

Up to 16 individuals belonging to 14 species of cones snails from genera Africonus, Varioconus, and Kalloconus were sampled. The venom gland was dissected and preserve din RNAlater. RNA was extracted and sequenced using Illumina 2x100. The reads were cleaned and assembled using Trinity. Annotation was performed against a custom reference dataset. Raw reads are deposite in SRA database (accession numbers SRR11807492-SRR11807507, Bioproject PRJNA631880). Here, we provide the following files: 1) "Conus_mitogenomes_alignment.phy", which has the alignment used for reconstructing the phylogenetic tree in Supp. Mat. Fig. 1; 2) "CAP_protein_alignment. phy", which has the alignment used for reconstructing the phylogenetic tree in Supp. Mat. Fig. 3; 3) "Conotoxins_Hormones_Proteins_aa.fasta", a list of the amino acid sequences of all the identified venom precursors in fasta format; 4) "Conotoxins_Hormones_Proteins_nt.fasta", a list of the nucleotide sequences of all the identified venom precursors in fasta format; 5) "Trinity_assemblies. zip", the outputs of Trinity with the assemblies of all the venom gland transcriptomes studied in the paper; 6) "BLAST_db_conotoxins.fasta", the reference database used to indetify and annotate the venom precursors; 7) "PCA-Composition_comparisons.zip", the inputs and outputs of the principal components anlyses shown in Fig. 3, Supp Mat Figs. 5 and 6; 8) "RSEM_and_EBSeq.zip", the inputs and outputs of the differential expression studies shown in Fig. 4.

Usage Notes

Species codes and abbreviations used in data files are summarized in the ReadMe.file

Funding

Ministerio de Economía y Competitividad, Award: CGL2013-45211-C2-2-P

Ministerio de Economía y Competitividad, Award: CGL2016-75255-C2-1-P

Ministerio de Economía y Competitividad, Award: BES-2014-069575