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Characterization of the Conus bullatus genome and its venom-duct transcriptome.

Hu H, Bandyopadhyay PK, Olivera BM, Yandell M - BMC Genomics (2011)

Bottom Line: Our results provide the first global view of venom-duct transcription in any cone snail.A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity.We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Eccles institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA.

ABSTRACT

Background: The venomous marine gastropods, cone snails (genus Conus), inject prey with a lethal cocktail of conopeptides, small cysteine-rich peptides, each with a high affinity for its molecular target, generally an ion channel, receptor or transporter. Over the last decade, conopeptides have proven indispensable reagents for the study of vertebrate neurotransmission. Conus bullatus belongs to a clade of Conus species called Textilia, whose pharmacology is still poorly characterized. Thus the genomics analyses presented here provide the first step toward a better understanding the enigmatic Textilia clade.

Results: We have carried out a sequencing survey of the Conus bullatus genome and venom-duct transcriptome. We find that conopeptides are highly expressed within the venom-duct, and describe an in silico pipeline for their discovery and characterization using RNA-seq data. We have also carried out low-coverage shotgun sequencing of the genome, and have used these data to determine its size, genome-wide base composition, simple repeat, and mobile element densities.

Conclusions: Our results provide the first global view of venom-duct transcription in any cone snail. A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity. We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.

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Comparison of Repetitive element counts in 1 million reads drawn from five different genomes. Repeats in 1 million randomly sampled C. bullatus Illumina 80-bp reads were characterized using RepeatMasker and compared to matched datasets manufactured from simulated reads from three other sequenced genomes and real reads from Flatley genome. X-axis: repeat-class. Y-axis: counts.
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Figure 2: Comparison of Repetitive element counts in 1 million reads drawn from five different genomes. Repeats in 1 million randomly sampled C. bullatus Illumina 80-bp reads were characterized using RepeatMasker and compared to matched datasets manufactured from simulated reads from three other sequenced genomes and real reads from Flatley genome. X-axis: repeat-class. Y-axis: counts.

Mentions: We took three approaches to characterize the repeat content of the C. bullatus genome. First, we ran RepeatMasker on 1 million randomly selected C. bullatus genomic reads, comparing the results to a matched human, Caenorhabditis elegans, Drosophila melanogaster, and Aplysia californica (a mollusk) datasets of simulated reads, as well as real human genome reads[30] (see Methods for details); these datasets match the Conus data precisely as regards number of reads, distance between pairs, read lengths, and (among the simulated sets) base quality (see Methods for details). Comparisons of the simulated human reads to real human reads (purple and grey columns in Figure 2), indicates that the simulated human reads closely match the real reads as regards repeat content for all repeat classes except simple repeats. We speculate that this is because many simple repeats (e.g., those near telomeres and centromeres) are designated as "N" in the reference human genome; hence, a random sampling of segments of the human reference assembly under represents its simple repeat content.


Characterization of the Conus bullatus genome and its venom-duct transcriptome.

Hu H, Bandyopadhyay PK, Olivera BM, Yandell M - BMC Genomics (2011)

Comparison of Repetitive element counts in 1 million reads drawn from five different genomes. Repeats in 1 million randomly sampled C. bullatus Illumina 80-bp reads were characterized using RepeatMasker and compared to matched datasets manufactured from simulated reads from three other sequenced genomes and real reads from Flatley genome. X-axis: repeat-class. Y-axis: counts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040727&req=5

Figure 2: Comparison of Repetitive element counts in 1 million reads drawn from five different genomes. Repeats in 1 million randomly sampled C. bullatus Illumina 80-bp reads were characterized using RepeatMasker and compared to matched datasets manufactured from simulated reads from three other sequenced genomes and real reads from Flatley genome. X-axis: repeat-class. Y-axis: counts.
Mentions: We took three approaches to characterize the repeat content of the C. bullatus genome. First, we ran RepeatMasker on 1 million randomly selected C. bullatus genomic reads, comparing the results to a matched human, Caenorhabditis elegans, Drosophila melanogaster, and Aplysia californica (a mollusk) datasets of simulated reads, as well as real human genome reads[30] (see Methods for details); these datasets match the Conus data precisely as regards number of reads, distance between pairs, read lengths, and (among the simulated sets) base quality (see Methods for details). Comparisons of the simulated human reads to real human reads (purple and grey columns in Figure 2), indicates that the simulated human reads closely match the real reads as regards repeat content for all repeat classes except simple repeats. We speculate that this is because many simple repeats (e.g., those near telomeres and centromeres) are designated as "N" in the reference human genome; hence, a random sampling of segments of the human reference assembly under represents its simple repeat content.

Bottom Line: Our results provide the first global view of venom-duct transcription in any cone snail.A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity.We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Eccles institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA.

ABSTRACT

Background: The venomous marine gastropods, cone snails (genus Conus), inject prey with a lethal cocktail of conopeptides, small cysteine-rich peptides, each with a high affinity for its molecular target, generally an ion channel, receptor or transporter. Over the last decade, conopeptides have proven indispensable reagents for the study of vertebrate neurotransmission. Conus bullatus belongs to a clade of Conus species called Textilia, whose pharmacology is still poorly characterized. Thus the genomics analyses presented here provide the first step toward a better understanding the enigmatic Textilia clade.

Results: We have carried out a sequencing survey of the Conus bullatus genome and venom-duct transcriptome. We find that conopeptides are highly expressed within the venom-duct, and describe an in silico pipeline for their discovery and characterization using RNA-seq data. We have also carried out low-coverage shotgun sequencing of the genome, and have used these data to determine its size, genome-wide base composition, simple repeat, and mobile element densities.

Conclusions: Our results provide the first global view of venom-duct transcription in any cone snail. A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity. We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.

Show MeSH