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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 expression of phospholipases A2 was uniform across transcripts inMicrurus fulvius. The phospholipase A2 (PLA2) gene family was characterized by an even distribution of expression levels. A homologous toxin sequence from the eastern diamondback rattlesnake (Crotalus adamanteus) was used as an outgroup to root the phylogeny. The root branch was shortened for visual clarity and is indicated by the dashed line. Bayesian posterior probability values exceeding 50% are shown. Adjacent bars indicate expression levels relative to the most highly expressed member of the class, with a completely filled bar indicating the most highly expressed transcript of the class. (A) A maximum-likelihood phylogeny of M. fulvius PLA2 clusters under the SYM+G model. PLA2 expression levels were much more evenly distributed throughout the class in comparison to 3FTx transcript expression levels (Figure 4). (B) A maximum-likelihood phylogeny of M. fulvius transcripts identified in this study as well as orthologous PLA2 transcripts from M. corallinus and M. altirostris under the SYM+G model. Tips are color-coded by species. The sub-clade containing the M. altirostris transcripts again suggests divergence among toxins may occur following speciation events.
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Figure 4: The expression of phospholipases A2 was uniform across transcripts inMicrurus fulvius. The phospholipase A2 (PLA2) gene family was characterized by an even distribution of expression levels. A homologous toxin sequence from the eastern diamondback rattlesnake (Crotalus adamanteus) was used as an outgroup to root the phylogeny. The root branch was shortened for visual clarity and is indicated by the dashed line. Bayesian posterior probability values exceeding 50% are shown. Adjacent bars indicate expression levels relative to the most highly expressed member of the class, with a completely filled bar indicating the most highly expressed transcript of the class. (A) A maximum-likelihood phylogeny of M. fulvius PLA2 clusters under the SYM+G model. PLA2 expression levels were much more evenly distributed throughout the class in comparison to 3FTx transcript expression levels (Figure 4). (B) A maximum-likelihood phylogeny of M. fulvius transcripts identified in this study as well as orthologous PLA2 transcripts from M. corallinus and M. altirostris under the SYM+G model. Tips are color-coded by species. The sub-clade containing the M. altirostris transcripts again suggests divergence among toxins may occur following speciation events.

Mentions: A maximum-likelihood phylogeny for 31 unique M. fulvius PLA2 clusters was estimated under the SYM+G model (Figure 4A). Expression levels for PLA2 transcripts were much more evenly distributed across the entire gene family in comparison to 3FTx sequences. The most highly expressed 3FTx transcript, 3FTx-2a, accounted for 22.7% of the total 3FTx reads while four transcripts accounted for approximately 67.0% of the 3FTx reads. In the PLA2 gene family, PLA2-2a was the most abundant toxin family member, accounting for 8.3% of the total PLA2 reads and the four most highly expressed transcripts accounted for only 30.8% of the reads mapping to PLA2s. Although these two families dominated toxin transcript expression levels in the M. fulvius venom gland, PLA2s did so through uniform expression while 3FTx expression patterns were tremendously biased. PLA2 transcripts also demonstrated less sequence divergence among clusters relative to 3FTx sequences. PLA2s are esterolytic enzymes that share a conserved three-dimensional structure [4,20], and the greater similarity between PLA2 transcripts may be a result of more stringent conformational constraints. The conservation of crucial structures in PLA2 enzymes ensures a functioning active site whereas the relatively short 3FTx peptides may be free of this limitation. Lynch [4] found that functionally critical sites were under strong purifying selection in PLA2s, with strong directional selection being restricted to surface residues due to their interactions with specific targets in prey, enabling prey-specific adaptation while ensuring the functionality of the enzyme. The maximum-likelihood phylogeny for 31 M. fulvius PLA2 clusters, three M. altirostris sequences, and a single M. corallinus sequence was estimated under the SYM+G model (Figure 4B). Functional divergence among PLA2s may also occur following speciation events [4], as all three M. altirostris sequences constitute a monophyletic clade and are sister to PLA2-21, a transcript that accounts for <1% of PLA2 reads in M. fulvius (although the pattern is not as strong as in 3FTxs as the PLA2-21/ M. altirostris clade is not well-supported).


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 expression of phospholipases A2 was uniform across transcripts inMicrurus fulvius. The phospholipase A2 (PLA2) gene family was characterized by an even distribution of expression levels. A homologous toxin sequence from the eastern diamondback rattlesnake (Crotalus adamanteus) was used as an outgroup to root the phylogeny. The root branch was shortened for visual clarity and is indicated by the dashed line. Bayesian posterior probability values exceeding 50% are shown. Adjacent bars indicate expression levels relative to the most highly expressed member of the class, with a completely filled bar indicating the most highly expressed transcript of the class. (A) A maximum-likelihood phylogeny of M. fulvius PLA2 clusters under the SYM+G model. PLA2 expression levels were much more evenly distributed throughout the class in comparison to 3FTx transcript expression levels (Figure 4). (B) A maximum-likelihood phylogeny of M. fulvius transcripts identified in this study as well as orthologous PLA2 transcripts from M. corallinus and M. altirostris under the SYM+G model. Tips are color-coded by species. The sub-clade containing the M. altirostris transcripts again suggests divergence among toxins may occur following speciation events.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 4: The expression of phospholipases A2 was uniform across transcripts inMicrurus fulvius. The phospholipase A2 (PLA2) gene family was characterized by an even distribution of expression levels. A homologous toxin sequence from the eastern diamondback rattlesnake (Crotalus adamanteus) was used as an outgroup to root the phylogeny. The root branch was shortened for visual clarity and is indicated by the dashed line. Bayesian posterior probability values exceeding 50% are shown. Adjacent bars indicate expression levels relative to the most highly expressed member of the class, with a completely filled bar indicating the most highly expressed transcript of the class. (A) A maximum-likelihood phylogeny of M. fulvius PLA2 clusters under the SYM+G model. PLA2 expression levels were much more evenly distributed throughout the class in comparison to 3FTx transcript expression levels (Figure 4). (B) A maximum-likelihood phylogeny of M. fulvius transcripts identified in this study as well as orthologous PLA2 transcripts from M. corallinus and M. altirostris under the SYM+G model. Tips are color-coded by species. The sub-clade containing the M. altirostris transcripts again suggests divergence among toxins may occur following speciation events.
Mentions: A maximum-likelihood phylogeny for 31 unique M. fulvius PLA2 clusters was estimated under the SYM+G model (Figure 4A). Expression levels for PLA2 transcripts were much more evenly distributed across the entire gene family in comparison to 3FTx sequences. The most highly expressed 3FTx transcript, 3FTx-2a, accounted for 22.7% of the total 3FTx reads while four transcripts accounted for approximately 67.0% of the 3FTx reads. In the PLA2 gene family, PLA2-2a was the most abundant toxin family member, accounting for 8.3% of the total PLA2 reads and the four most highly expressed transcripts accounted for only 30.8% of the reads mapping to PLA2s. Although these two families dominated toxin transcript expression levels in the M. fulvius venom gland, PLA2s did so through uniform expression while 3FTx expression patterns were tremendously biased. PLA2 transcripts also demonstrated less sequence divergence among clusters relative to 3FTx sequences. PLA2s are esterolytic enzymes that share a conserved three-dimensional structure [4,20], and the greater similarity between PLA2 transcripts may be a result of more stringent conformational constraints. The conservation of crucial structures in PLA2 enzymes ensures a functioning active site whereas the relatively short 3FTx peptides may be free of this limitation. Lynch [4] found that functionally critical sites were under strong purifying selection in PLA2s, with strong directional selection being restricted to surface residues due to their interactions with specific targets in prey, enabling prey-specific adaptation while ensuring the functionality of the enzyme. The maximum-likelihood phylogeny for 31 M. fulvius PLA2 clusters, three M. altirostris sequences, and a single M. corallinus sequence was estimated under the SYM+G model (Figure 4B). Functional divergence among PLA2s may also occur following speciation events [4], as all three M. altirostris sequences constitute a monophyletic clade and are sister to PLA2-21, a transcript that accounts for <1% of PLA2 reads in M. fulvius (although the pattern is not as strong as in 3FTxs as the PLA2-21/ M. altirostris clade is not well-supported).

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