Limits...
De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species.

Bouzid W, Verdenaud M, Klopp C, Ducancel F, Noirot C, Vétillard A - BMC Genomics (2014)

Bottom Line: Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue.To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal.In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.

View Article: PubMed Central - PubMed

Affiliation: Venoms and Biological Activities Laboratory, EA 4357, PRES-University of Toulouse, Jean-François Champollion University Center, Albi, France. angelique.vetillard@univ-jfc.fr.

ABSTRACT

Background: Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the composition and the potential that these biomolecules could represent. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput approach using Illumina technology has been applied to analyze the genes expressed in active venom glands of this ant species.

Results: A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%), followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue. Finally, about 40% of the generated contigs have no hits in the databases with 25% of the predicted peptides bearing signal peptide emphasizing the potential of the investigation of these sequences as source of new molecules. Among these contigs, six putative novel peptides that show homologies with previously identified antimicrobial peptides were identified.

Conclusions: To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal. In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.

Show MeSH

Related in: MedlinePlus

Gene ontology (GO) functional categorization of the generated sequences fromT. bicarinatumvenom glands. A: GO terms assigned in relation to the molecular function, B: GO terms assigned according to the biological process.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4256838&req=5

Fig2: Gene ontology (GO) functional categorization of the generated sequences fromT. bicarinatumvenom glands. A: GO terms assigned in relation to the molecular function, B: GO terms assigned according to the biological process.

Mentions: The gene expression profile of Tetramorium bicarinatum venom glands were deduced from mRNA samples of ant whole body and venom gland tissues using the Illumina sequencing approach. After the sequencing quality filtering step, a total of 424,743,516 of 100-base-pair Illumina reads were obtained for both samples (Table 1). The de novo assemblies yielded 37,818 contigs for the two libraries (venom glands and ant carcasses) among which 33,241 contigs were shared by both tissues (Figure 1). All unassembled sequencing reads, which accounted for 25% for the ant library and 50% for the venom gland library, were excluded from our investigation. As the aim of this study was to profile venom transcriptome, we mainly focus on the 36,042 contigs recovered from the venom gland library. The contigs recorded from the ant whole body sample were used to assess differentially expressed genes. Among these detected transcripts (contigs), 27,873 have at least one predicted ORF with 59.77% producing significant hits in the available databases. Gene ontology (GO) functional categorization of the annotated contigs from T. bicarinatum venom glands is provided on Figure 2. The GO analysis in relation to molecular functions revealed that the largest number of transcripts was related to protein binding, followed by catalytic activities and at a lower rate to structural protein and transporter activities (Figure 2A). Analysis of the biological processes revealed two dominant major gene categories of cellular and metabolic processes. The following categories are related to biological regulation, localization, response to stimulus, biogenesis and signaling (Figure 2B).Table 1


De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species.

Bouzid W, Verdenaud M, Klopp C, Ducancel F, Noirot C, Vétillard A - BMC Genomics (2014)

Gene ontology (GO) functional categorization of the generated sequences fromT. bicarinatumvenom glands. A: GO terms assigned in relation to the molecular function, B: GO terms assigned according to the biological process.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4256838&req=5

Fig2: Gene ontology (GO) functional categorization of the generated sequences fromT. bicarinatumvenom glands. A: GO terms assigned in relation to the molecular function, B: GO terms assigned according to the biological process.
Mentions: The gene expression profile of Tetramorium bicarinatum venom glands were deduced from mRNA samples of ant whole body and venom gland tissues using the Illumina sequencing approach. After the sequencing quality filtering step, a total of 424,743,516 of 100-base-pair Illumina reads were obtained for both samples (Table 1). The de novo assemblies yielded 37,818 contigs for the two libraries (venom glands and ant carcasses) among which 33,241 contigs were shared by both tissues (Figure 1). All unassembled sequencing reads, which accounted for 25% for the ant library and 50% for the venom gland library, were excluded from our investigation. As the aim of this study was to profile venom transcriptome, we mainly focus on the 36,042 contigs recovered from the venom gland library. The contigs recorded from the ant whole body sample were used to assess differentially expressed genes. Among these detected transcripts (contigs), 27,873 have at least one predicted ORF with 59.77% producing significant hits in the available databases. Gene ontology (GO) functional categorization of the annotated contigs from T. bicarinatum venom glands is provided on Figure 2. The GO analysis in relation to molecular functions revealed that the largest number of transcripts was related to protein binding, followed by catalytic activities and at a lower rate to structural protein and transporter activities (Figure 2A). Analysis of the biological processes revealed two dominant major gene categories of cellular and metabolic processes. The following categories are related to biological regulation, localization, response to stimulus, biogenesis and signaling (Figure 2B).Table 1

Bottom Line: Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue.To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal.In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.

View Article: PubMed Central - PubMed

Affiliation: Venoms and Biological Activities Laboratory, EA 4357, PRES-University of Toulouse, Jean-François Champollion University Center, Albi, France. angelique.vetillard@univ-jfc.fr.

ABSTRACT

Background: Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the composition and the potential that these biomolecules could represent. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput approach using Illumina technology has been applied to analyze the genes expressed in active venom glands of this ant species.

Results: A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%), followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue. Finally, about 40% of the generated contigs have no hits in the databases with 25% of the predicted peptides bearing signal peptide emphasizing the potential of the investigation of these sequences as source of new molecules. Among these contigs, six putative novel peptides that show homologies with previously identified antimicrobial peptides were identified.

Conclusions: To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal. In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.

Show MeSH
Related in: MedlinePlus