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Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails.

Gorson J, Ramrattan G, Verdes A, Wright EM, Kantor Y, Rajaram Srinivasan R, Musunuri R, Packer D, Albano G, Qiu WG, Holford M - Genome Biol Evol (2015)

Bottom Line: Phylogenetic methodology was used to identify 14 teretoxin gene superfamilies for the first time, 13 of which are unique to the Terebridae.Additionally, basic local algorithm search tool homology-based searches to venom-related genes and posttranslational modification enzymes identified a convergence of certain venom proteins, such as actinoporin, commonly found in venoms.This research provides novel insights into venom evolution and recruitment in Conoidean predatory marine snails and identifies a plethora of terebrid venom peptides that can be used to investigate fundamental questions pertaining to gene evolution.

View Article: PubMed Central - PubMed

Affiliation: Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York.

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Venn diagram showing overlap of putative Tr. anilis teretoxins found in the four different assemblies. (A) Comparative analysis of the four assemblies conducted on Tr. anilis transcriptome sequences: VO25, Velvet Oases assembly with kmer25; TrinDN, Trinity digital normalization assembly; TrinAllReads, Trinity assembly without digital normalization; VO51, Velvet Oases assembly with kmer51. (B) Representative alignments of teretoxin transcripts found in all four, three, two, and only one assembly, respectively. Levels of support range from all four assemblies to single assembly (Tan, Tr. anilis).
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evv104-F3: Venn diagram showing overlap of putative Tr. anilis teretoxins found in the four different assemblies. (A) Comparative analysis of the four assemblies conducted on Tr. anilis transcriptome sequences: VO25, Velvet Oases assembly with kmer25; TrinDN, Trinity digital normalization assembly; TrinAllReads, Trinity assembly without digital normalization; VO51, Velvet Oases assembly with kmer51. (B) Representative alignments of teretoxin transcripts found in all four, three, two, and only one assembly, respectively. Levels of support range from all four assemblies to single assembly (Tan, Tr. anilis).

Mentions: A total of four Tr. anilis assemblies, including Trinity assemblies and Velvet Oases assemblies run at kmers 25 and 51, were used for the identification of novel neuropeptides. The four assemblies were: TrinDN (Trinity assembly from digitally normalized reads), TrinAllReads (Trinity assembly run on the full set of reads), VO25 (Velvet Oases assembly run at kmer = 25), and VO51 (Velvet Oases assembly run at kmer = 51) (fig. 3A). Four assemblies were used to maximize the capture of putative teretoxins, for comparative analyses across assemblies to support the de novo assembly process, and to determine which assembly process should be used in future pipelines. All assemblies identified putative teretoxins, however certain peptides were present only under certain assembly conditions, such as Tan22.5 (fig. 3B). Twenty-seven teretoxins were identified by all four assemblies of Tr. anilis, indicating these were the most valid T. anilis teretoxin transcripts. When directly comparing VO51 and Trinity de novo assembly statistics it would appear as if VO51 was the most effective assembly (supplementary table S1, Supplementary Material online). However, several recent studies have analyzed de novo sequencing assemblers and the validity of measures, such as median contig length, length of contigs, and N50, and found these statistics can be misleading. While generally assembly statistics can identify the continuity of contigs, they cannot attest to contig validity (Kumar and Blaxter 2010; Mundry et al. 2012; Salzberg et al. 2012; Clarke et al. 2013; Lu et al. 2013; O’Neil and Emrich 2013). Conversely, Trinity, which was designed to capture transcript isoforms, has been identified as the best assembler under reference-free conditions, such as with nonmodel systems like the Terebridae (Li et al. 2014). Additionally, when comparing the number of putative teretoxins identified, VO51 and Trinity assemblers found relatively the same number of contigs, 61 for VO51 versus 59 for TrinDN (Fig. 3A). As it is not practical to perform four assemblies for all transcriptomes of interest, the digitally normalized Trinity assembly was chosen as the primary tool for downstream analysis of Tr. anilis and was subsequently chosen as the primary tool for assembly and downstream analysis of Te. subulata. Having well validated high-quality sequence data is an essential first step to studying any transcriptome of interest. As there is no solved terebrid genome, de novo assembly is required. A significant effort was made to utilize multiple assembly programs and bioinformatics approaches for cross validation of findings and to achieve reliable assemblies of Tr. anilis and Te. subulata venom duct transcriptomes to obtain a reliable portrait of Terebridae venom.Fig. 3.—


Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails.

Gorson J, Ramrattan G, Verdes A, Wright EM, Kantor Y, Rajaram Srinivasan R, Musunuri R, Packer D, Albano G, Qiu WG, Holford M - Genome Biol Evol (2015)

Venn diagram showing overlap of putative Tr. anilis teretoxins found in the four different assemblies. (A) Comparative analysis of the four assemblies conducted on Tr. anilis transcriptome sequences: VO25, Velvet Oases assembly with kmer25; TrinDN, Trinity digital normalization assembly; TrinAllReads, Trinity assembly without digital normalization; VO51, Velvet Oases assembly with kmer51. (B) Representative alignments of teretoxin transcripts found in all four, three, two, and only one assembly, respectively. Levels of support range from all four assemblies to single assembly (Tan, Tr. anilis).
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evv104-F3: Venn diagram showing overlap of putative Tr. anilis teretoxins found in the four different assemblies. (A) Comparative analysis of the four assemblies conducted on Tr. anilis transcriptome sequences: VO25, Velvet Oases assembly with kmer25; TrinDN, Trinity digital normalization assembly; TrinAllReads, Trinity assembly without digital normalization; VO51, Velvet Oases assembly with kmer51. (B) Representative alignments of teretoxin transcripts found in all four, three, two, and only one assembly, respectively. Levels of support range from all four assemblies to single assembly (Tan, Tr. anilis).
Mentions: A total of four Tr. anilis assemblies, including Trinity assemblies and Velvet Oases assemblies run at kmers 25 and 51, were used for the identification of novel neuropeptides. The four assemblies were: TrinDN (Trinity assembly from digitally normalized reads), TrinAllReads (Trinity assembly run on the full set of reads), VO25 (Velvet Oases assembly run at kmer = 25), and VO51 (Velvet Oases assembly run at kmer = 51) (fig. 3A). Four assemblies were used to maximize the capture of putative teretoxins, for comparative analyses across assemblies to support the de novo assembly process, and to determine which assembly process should be used in future pipelines. All assemblies identified putative teretoxins, however certain peptides were present only under certain assembly conditions, such as Tan22.5 (fig. 3B). Twenty-seven teretoxins were identified by all four assemblies of Tr. anilis, indicating these were the most valid T. anilis teretoxin transcripts. When directly comparing VO51 and Trinity de novo assembly statistics it would appear as if VO51 was the most effective assembly (supplementary table S1, Supplementary Material online). However, several recent studies have analyzed de novo sequencing assemblers and the validity of measures, such as median contig length, length of contigs, and N50, and found these statistics can be misleading. While generally assembly statistics can identify the continuity of contigs, they cannot attest to contig validity (Kumar and Blaxter 2010; Mundry et al. 2012; Salzberg et al. 2012; Clarke et al. 2013; Lu et al. 2013; O’Neil and Emrich 2013). Conversely, Trinity, which was designed to capture transcript isoforms, has been identified as the best assembler under reference-free conditions, such as with nonmodel systems like the Terebridae (Li et al. 2014). Additionally, when comparing the number of putative teretoxins identified, VO51 and Trinity assemblers found relatively the same number of contigs, 61 for VO51 versus 59 for TrinDN (Fig. 3A). As it is not practical to perform four assemblies for all transcriptomes of interest, the digitally normalized Trinity assembly was chosen as the primary tool for downstream analysis of Tr. anilis and was subsequently chosen as the primary tool for assembly and downstream analysis of Te. subulata. Having well validated high-quality sequence data is an essential first step to studying any transcriptome of interest. As there is no solved terebrid genome, de novo assembly is required. A significant effort was made to utilize multiple assembly programs and bioinformatics approaches for cross validation of findings and to achieve reliable assemblies of Tr. anilis and Te. subulata venom duct transcriptomes to obtain a reliable portrait of Terebridae venom.Fig. 3.—

Bottom Line: Phylogenetic methodology was used to identify 14 teretoxin gene superfamilies for the first time, 13 of which are unique to the Terebridae.Additionally, basic local algorithm search tool homology-based searches to venom-related genes and posttranslational modification enzymes identified a convergence of certain venom proteins, such as actinoporin, commonly found in venoms.This research provides novel insights into venom evolution and recruitment in Conoidean predatory marine snails and identifies a plethora of terebrid venom peptides that can be used to investigate fundamental questions pertaining to gene evolution.

View Article: PubMed Central - PubMed

Affiliation: Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York.

Show MeSH