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The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms.

Margres MJ, Aronow K, Loyacano J, Rokyta DR - BMC Genomics (2013)

Bottom Line: New World coral snakes (Elapidae) are represented by three genera and over 120 species and subspecies that are capable of causing significant human morbidity and mortality, yet coral-snake venom composition is poorly understood in comparison to that of Old World elapids.Toxins exhibited high levels of heterozygosity relative to nontoxins, and overdominance may favor gene duplication leading to the fixation of advantageous alleles.Toxin gene duplication may be driven by heterozygote advantage, as the frequency of polymorphic toxin loci was significantly higher than that of nontoxins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA.

ABSTRACT

Background: Snake venom is shaped by the ecology and evolution of venomous species, and signals of positive selection in toxins have been consistently documented, reflecting the role of venoms as an ecologically critical phenotype. New World coral snakes (Elapidae) are represented by three genera and over 120 species and subspecies that are capable of causing significant human morbidity and mortality, yet coral-snake venom composition is poorly understood in comparison to that of Old World elapids. High-throughput sequencing is capable of identifying thousands of loci, while providing characterizations of expression patterns and the molecular evolutionary forces acting within the venom gland.

Results: We describe the de novo assembly and analysis of the venom-gland transcriptome of the eastern coral snake (Micrurus fulvius). We identified 1,950 nontoxin transcripts and 116 toxin transcripts. These transcripts accounted for 57.1% of the total reads, with toxins accounting for 45.8% of the total reads. Phospholipases A(2) and three-finger toxins dominated expression, accounting for 86.0% of the toxin reads. A total of 15 toxin families were identified, revealing venom complexity previously unknown from New World coral snakes. Toxins exhibited high levels of heterozygosity relative to nontoxins, and overdominance may favor gene duplication leading to the fixation of advantageous alleles. Phospholipase A(2) expression was uniformly distributed throughout the class while three-finger toxin expression was dominated by a handful of transcripts, and phylogenetic analyses indicate that toxin divergence may have occurred following speciation. Positive selection was detected in three of the four most diverse toxin classes, suggesting that venom diversification is driven by recurrent directional selection.

Conclusions: We describe the most complete characterization of an elapid venom gland to date. Toxin gene duplication may be driven by heterozygote advantage, as the frequency of polymorphic toxin loci was significantly higher than that of nontoxins. Diversification among toxins appeared to follow speciation reflecting species-specific adaptation, and this divergence may be directly related to dietary shifts and is suggestive of a coevolutionary arms race.

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The venom-gland transcriptome ofMicrurus fulvius was extremely biased towards toxin production. The venom-gland transcriptome of M. fulvius was dominated by toxin transcripts and, in particular, phospholipases A2 (PLA2s). (A) A total of 1,950 nontoxin-encoding and 116 toxin-encoding transcripts were identified. Toxins were grouped into 75 clusters based on <1% nucleotide divergence. The inset shows a magnification of the top 200 transcripts, the vast majority of which code for toxins. (B) Expression levels of individual toxin clusters, color coded by toxin class. The 75 toxin clusters represent 15 distinct toxin classes. Three-finger toxin and PLA2 transcripts dominated toxin expression levels, accounting for nearly 86% of all toxin reads. Toxin-class abbreviations are as follows: 3FTx: three-finger toxin; CTL: C-type lectin; CREGF: cysteine-rich with EGF-like domain; HYAL: hyaluronidase; KUN: Kunitz-type protease inhibitor; LAAO: L amino-acid oxidase; LCN: long-chain neurotoxin; NGF: nerve growth factor; NP: natriuretic peptide; NUC: nucleotidase; PDE: phosphodiesterase; PLA2: phospholipase A2; PLB: phospholipase B; SVMP: snake venom metalloproteinase; VEGF: vascular endothelial growth factor.
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Figure 1: The venom-gland transcriptome ofMicrurus fulvius was extremely biased towards toxin production. The venom-gland transcriptome of M. fulvius was dominated by toxin transcripts and, in particular, phospholipases A2 (PLA2s). (A) A total of 1,950 nontoxin-encoding and 116 toxin-encoding transcripts were identified. Toxins were grouped into 75 clusters based on <1% nucleotide divergence. The inset shows a magnification of the top 200 transcripts, the vast majority of which code for toxins. (B) Expression levels of individual toxin clusters, color coded by toxin class. The 75 toxin clusters represent 15 distinct toxin classes. Three-finger toxin and PLA2 transcripts dominated toxin expression levels, accounting for nearly 86% of all toxin reads. Toxin-class abbreviations are as follows: 3FTx: three-finger toxin; CTL: C-type lectin; CREGF: cysteine-rich with EGF-like domain; HYAL: hyaluronidase; KUN: Kunitz-type protease inhibitor; LAAO: L amino-acid oxidase; LCN: long-chain neurotoxin; NGF: nerve growth factor; NP: natriuretic peptide; NUC: nucleotidase; PDE: phosphodiesterase; PLA2: phospholipase A2; PLB: phospholipase B; SVMP: snake venom metalloproteinase; VEGF: vascular endothelial growth factor.

Mentions: Our high-throughput transcriptomic analysis revealed high venom complexity in M. fulvius, comparable to the diversity of toxin components recently identified in the venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus: Viperidae) [16]. We generated 79,573,048 pairs of 100 nucleotide raw reads and merged 61,609,456 pairs on the basis of overlap at their 3’ ends, following the approach of Rokyta et al. [16] and Rodrigue et al. [17]. These merged reads had an average length of 134 nucleotides with average phred scores of 46. The iterative assembly process described by Rokyta et al. [16] coupled with a reference-based assembly using nontoxin transcripts previously described in the venom-gland transcriptome of C. adamanteus resulted in the identification of 1,950 unique, full-length nontoxin coding sequences and 116 unique, full-length toxin coding transcripts (Figure 1A).


The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms.

Margres MJ, Aronow K, Loyacano J, Rokyta DR - BMC Genomics (2013)

The venom-gland transcriptome ofMicrurus fulvius was extremely biased towards toxin production. The venom-gland transcriptome of M. fulvius was dominated by toxin transcripts and, in particular, phospholipases A2 (PLA2s). (A) A total of 1,950 nontoxin-encoding and 116 toxin-encoding transcripts were identified. Toxins were grouped into 75 clusters based on <1% nucleotide divergence. The inset shows a magnification of the top 200 transcripts, the vast majority of which code for toxins. (B) Expression levels of individual toxin clusters, color coded by toxin class. The 75 toxin clusters represent 15 distinct toxin classes. Three-finger toxin and PLA2 transcripts dominated toxin expression levels, accounting for nearly 86% of all toxin reads. Toxin-class abbreviations are as follows: 3FTx: three-finger toxin; CTL: C-type lectin; CREGF: cysteine-rich with EGF-like domain; HYAL: hyaluronidase; KUN: Kunitz-type protease inhibitor; LAAO: L amino-acid oxidase; LCN: long-chain neurotoxin; NGF: nerve growth factor; NP: natriuretic peptide; NUC: nucleotidase; PDE: phosphodiesterase; PLA2: phospholipase A2; PLB: phospholipase B; SVMP: snake venom metalloproteinase; VEGF: vascular endothelial growth factor.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750283&req=5

Figure 1: The venom-gland transcriptome ofMicrurus fulvius was extremely biased towards toxin production. The venom-gland transcriptome of M. fulvius was dominated by toxin transcripts and, in particular, phospholipases A2 (PLA2s). (A) A total of 1,950 nontoxin-encoding and 116 toxin-encoding transcripts were identified. Toxins were grouped into 75 clusters based on <1% nucleotide divergence. The inset shows a magnification of the top 200 transcripts, the vast majority of which code for toxins. (B) Expression levels of individual toxin clusters, color coded by toxin class. The 75 toxin clusters represent 15 distinct toxin classes. Three-finger toxin and PLA2 transcripts dominated toxin expression levels, accounting for nearly 86% of all toxin reads. Toxin-class abbreviations are as follows: 3FTx: three-finger toxin; CTL: C-type lectin; CREGF: cysteine-rich with EGF-like domain; HYAL: hyaluronidase; KUN: Kunitz-type protease inhibitor; LAAO: L amino-acid oxidase; LCN: long-chain neurotoxin; NGF: nerve growth factor; NP: natriuretic peptide; NUC: nucleotidase; PDE: phosphodiesterase; PLA2: phospholipase A2; PLB: phospholipase B; SVMP: snake venom metalloproteinase; VEGF: vascular endothelial growth factor.
Mentions: Our high-throughput transcriptomic analysis revealed high venom complexity in M. fulvius, comparable to the diversity of toxin components recently identified in the venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus: Viperidae) [16]. We generated 79,573,048 pairs of 100 nucleotide raw reads and merged 61,609,456 pairs on the basis of overlap at their 3’ ends, following the approach of Rokyta et al. [16] and Rodrigue et al. [17]. These merged reads had an average length of 134 nucleotides with average phred scores of 46. The iterative assembly process described by Rokyta et al. [16] coupled with a reference-based assembly using nontoxin transcripts previously described in the venom-gland transcriptome of C. adamanteus resulted in the identification of 1,950 unique, full-length nontoxin coding sequences and 116 unique, full-length toxin coding transcripts (Figure 1A).

Bottom Line: New World coral snakes (Elapidae) are represented by three genera and over 120 species and subspecies that are capable of causing significant human morbidity and mortality, yet coral-snake venom composition is poorly understood in comparison to that of Old World elapids.Toxins exhibited high levels of heterozygosity relative to nontoxins, and overdominance may favor gene duplication leading to the fixation of advantageous alleles.Toxin gene duplication may be driven by heterozygote advantage, as the frequency of polymorphic toxin loci was significantly higher than that of nontoxins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA.

ABSTRACT

Background: Snake venom is shaped by the ecology and evolution of venomous species, and signals of positive selection in toxins have been consistently documented, reflecting the role of venoms as an ecologically critical phenotype. New World coral snakes (Elapidae) are represented by three genera and over 120 species and subspecies that are capable of causing significant human morbidity and mortality, yet coral-snake venom composition is poorly understood in comparison to that of Old World elapids. High-throughput sequencing is capable of identifying thousands of loci, while providing characterizations of expression patterns and the molecular evolutionary forces acting within the venom gland.

Results: We describe the de novo assembly and analysis of the venom-gland transcriptome of the eastern coral snake (Micrurus fulvius). We identified 1,950 nontoxin transcripts and 116 toxin transcripts. These transcripts accounted for 57.1% of the total reads, with toxins accounting for 45.8% of the total reads. Phospholipases A(2) and three-finger toxins dominated expression, accounting for 86.0% of the toxin reads. A total of 15 toxin families were identified, revealing venom complexity previously unknown from New World coral snakes. Toxins exhibited high levels of heterozygosity relative to nontoxins, and overdominance may favor gene duplication leading to the fixation of advantageous alleles. Phospholipase A(2) expression was uniformly distributed throughout the class while three-finger toxin expression was dominated by a handful of transcripts, and phylogenetic analyses indicate that toxin divergence may have occurred following speciation. Positive selection was detected in three of the four most diverse toxin classes, suggesting that venom diversification is driven by recurrent directional selection.

Conclusions: We describe the most complete characterization of an elapid venom gland to date. Toxin gene duplication may be driven by heterozygote advantage, as the frequency of polymorphic toxin loci was significantly higher than that of nontoxins. Diversification among toxins appeared to follow speciation reflecting species-specific adaptation, and this divergence may be directly related to dietary shifts and is suggestive of a coevolutionary arms race.

Show MeSH
Related in: MedlinePlus