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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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Profile of proportion of the genomic sequences with each copy number. Generated from all-by-all blast analysis of one million C. bullatus and H.sapiens reads each against themselves. The number of read partners is converted to copy-number of corresponding genomic sequence. X-axis: each bin's label gives the minimum and maximum copy numbers in the genome. Y-axis: fraction of reads falling into that bin.
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Figure 3: Profile of proportion of the genomic sequences with each copy number. Generated from all-by-all blast analysis of one million C. bullatus and H.sapiens reads each against themselves. The number of read partners is converted to copy-number of corresponding genomic sequence. X-axis: each bin's label gives the minimum and maximum copy numbers in the genome. Y-axis: fraction of reads falling into that bin.

Mentions: Because novel forms of retro-transposons might not have been identified in our RepeatMasker experiment, or some unknown bias in the ABySS [34] assembler might have caused us to underestimate the numbers of novel repeats identified with RECON, we devised a third experiment, that controls for both of these possibilities. In this experiment, we took the same read-datasets used in our RepeatMasker analysis (Figure 2), and performed an all-against-all BLAST [35] search of the C. bullatus reads against themselves, and repeated the same experiment for a matched set of simulated reads from H. sapiens (see Methods for details). For reasons of computational complexity we choose to limit this analysis to only one target genome: H. sapiens, because it is the most repeat rich of any in our dataset and its genome is nearly the same size as the C. bullatus genome. We then tallied the percentage of reads having one BLAST hit, two hits and so on. For each read, its number of hits can be used to obtain an estimate of the copy-number of its sequence within the genome (see Methods). This allows us to estimate the proportion of high-copy number genomic sequences within the Conus genome and to make comparisons to the human genome (Figure 3). This experiment presumes no prior knowledge of the repeat content of the genome. We also used the 'SEG' option with WU-BLAST [36] to exclude hits between reads consisting only of low complexity and/or simple sequence repeats. By using BLAST with the SEG option any reads consisting entirely of low complexity or simple sequence repeats will have no hits.


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

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

Profile of proportion of the genomic sequences with each copy number. Generated from all-by-all blast analysis of one million C. bullatus and H.sapiens reads each against themselves. The number of read partners is converted to copy-number of corresponding genomic sequence. X-axis: each bin's label gives the minimum and maximum copy numbers in the genome. Y-axis: fraction of reads falling into that bin.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Profile of proportion of the genomic sequences with each copy number. Generated from all-by-all blast analysis of one million C. bullatus and H.sapiens reads each against themselves. The number of read partners is converted to copy-number of corresponding genomic sequence. X-axis: each bin's label gives the minimum and maximum copy numbers in the genome. Y-axis: fraction of reads falling into that bin.
Mentions: Because novel forms of retro-transposons might not have been identified in our RepeatMasker experiment, or some unknown bias in the ABySS [34] assembler might have caused us to underestimate the numbers of novel repeats identified with RECON, we devised a third experiment, that controls for both of these possibilities. In this experiment, we took the same read-datasets used in our RepeatMasker analysis (Figure 2), and performed an all-against-all BLAST [35] search of the C. bullatus reads against themselves, and repeated the same experiment for a matched set of simulated reads from H. sapiens (see Methods for details). For reasons of computational complexity we choose to limit this analysis to only one target genome: H. sapiens, because it is the most repeat rich of any in our dataset and its genome is nearly the same size as the C. bullatus genome. We then tallied the percentage of reads having one BLAST hit, two hits and so on. For each read, its number of hits can be used to obtain an estimate of the copy-number of its sequence within the genome (see Methods). This allows us to estimate the proportion of high-copy number genomic sequences within the Conus genome and to make comparisons to the human genome (Figure 3). This experiment presumes no prior knowledge of the repeat content of the genome. We also used the 'SEG' option with WU-BLAST [36] to exclude hits between reads consisting only of low complexity and/or simple sequence repeats. By using BLAST with the SEG option any reads consisting entirely of low complexity or simple sequence repeats will have no hits.

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
Related in: MedlinePlus