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A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus.

Ranganathan S, Nagaraj SH, Hu M, Strube C, Schnieder T, Gasser RB - BMC Genomics (2007)

Bottom Line: They cause pathological effects and clinical disease in various ruminant hosts, particularly in young animals.The genes discovered in this study should assist research toward a better understanding of the basic molecular biology of D. viviparus, which could lead, in the longer term, to novel intervention strategies.The characterization of the D. viviparus transcriptome also provides a foundation for whole genome sequence analysis and future comparative transcriptomic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia. shoba.ranganathan@mq.edu.au

ABSTRACT

Background: Lungworms of the genus Dictyocaulus (family Dictyocaulidae) are parasitic nematodes of major economic importance. They cause pathological effects and clinical disease in various ruminant hosts, particularly in young animals. Dictyocaulus viviparus, called the bovine lungworm, is a major pathogen of cattle, with severe infections being fatal. In this study, we provide first insights into the transcriptome of the adult stage of D. viviparus through the analysis of expressed sequence tags (ESTs).

Results: Using our EST analysis pipeline, we estimate that the present dataset of 4436 ESTs is derived from 2258 genes based on cluster and comparative genomic analyses of the ESTs. Of the 2258 representative ESTs, 1159 (51.3%) had homologues in the free-living nematode C. elegans, 1174 (51.9%) in parasitic nematodes, 827 (36.6%) in organisms other than nematodes, and 863 (38%) had no significant match to any sequence in the current databases. Of the C. elegans homologues, 569 had observed 'non-wildtype' RNAi phenotypes, including embryonic lethality, maternal sterility, sterility in progeny, larval arrest and slow growth. We could functionally classify 776 (35%) sequences using the Gene Ontologies (GO) and established pathway associations to 696 (31%) sequences in Kyoto Encyclopedia of Genes and Genomes (KEGG). In addition, we predicted 85 secreted proteins which could represent potential candidates for developing novel anthelmintics or vaccines.

Conclusion: The bioinformatic analyses of ESTs data for D. viviparus has elucidated sets of relatively conserved and potentially novel genes. The genes discovered in this study should assist research toward a better understanding of the basic molecular biology of D. viviparus, which could lead, in the longer term, to novel intervention strategies. The characterization of the D. viviparus transcriptome also provides a foundation for whole genome sequence analysis and future comparative transcriptomic analyses.

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Bioinformatics analysis of D. viviparus ESTs. ESTExplorer analysis comprising Phases I (pre-processing), II (DNA-level annotation) and III (protein-level annotation), were augmented by homologue identification from nematodes as well as parasitic nematodes, using specialized databases.
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Figure 1: Bioinformatics analysis of D. viviparus ESTs. ESTExplorer analysis comprising Phases I (pre-processing), II (DNA-level annotation) and III (protein-level annotation), were augmented by homologue identification from nematodes as well as parasitic nematodes, using specialized databases.

Mentions: Of 5271 clones sequenced, a total of 4436 quality ESTs were obtained (Phase I, Figure 1), achieving a sequencing success of 84% (Table 1), which is consistent with previous studies [14,15]. These pre-processed ESTs ranged from 80–1164 bp, with a mean of 730 bp and a standard deviation (S.D.) of 258 bp. After clustering, the mean length of the contigs (or consensus sequences) increased to 787 (+/- 313) bp. The G+C content of the coding sequences was 43.5%, consistent with other nematodes from clade V [16,17] and slightly more than C. elegans (37%) and its congener, C. briggsae (38%) [18]. Under the assumption that the D. viviparus genome codes for ~22,000 proteins [19], the EST clusters were predicted to represent ~10–15% of the proteins encoded by this genome.


A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus.

Ranganathan S, Nagaraj SH, Hu M, Strube C, Schnieder T, Gasser RB - BMC Genomics (2007)

Bioinformatics analysis of D. viviparus ESTs. ESTExplorer analysis comprising Phases I (pre-processing), II (DNA-level annotation) and III (protein-level annotation), were augmented by homologue identification from nematodes as well as parasitic nematodes, using specialized databases.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2131760&req=5

Figure 1: Bioinformatics analysis of D. viviparus ESTs. ESTExplorer analysis comprising Phases I (pre-processing), II (DNA-level annotation) and III (protein-level annotation), were augmented by homologue identification from nematodes as well as parasitic nematodes, using specialized databases.
Mentions: Of 5271 clones sequenced, a total of 4436 quality ESTs were obtained (Phase I, Figure 1), achieving a sequencing success of 84% (Table 1), which is consistent with previous studies [14,15]. These pre-processed ESTs ranged from 80–1164 bp, with a mean of 730 bp and a standard deviation (S.D.) of 258 bp. After clustering, the mean length of the contigs (or consensus sequences) increased to 787 (+/- 313) bp. The G+C content of the coding sequences was 43.5%, consistent with other nematodes from clade V [16,17] and slightly more than C. elegans (37%) and its congener, C. briggsae (38%) [18]. Under the assumption that the D. viviparus genome codes for ~22,000 proteins [19], the EST clusters were predicted to represent ~10–15% of the proteins encoded by this genome.

Bottom Line: They cause pathological effects and clinical disease in various ruminant hosts, particularly in young animals.The genes discovered in this study should assist research toward a better understanding of the basic molecular biology of D. viviparus, which could lead, in the longer term, to novel intervention strategies.The characterization of the D. viviparus transcriptome also provides a foundation for whole genome sequence analysis and future comparative transcriptomic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia. shoba.ranganathan@mq.edu.au

ABSTRACT

Background: Lungworms of the genus Dictyocaulus (family Dictyocaulidae) are parasitic nematodes of major economic importance. They cause pathological effects and clinical disease in various ruminant hosts, particularly in young animals. Dictyocaulus viviparus, called the bovine lungworm, is a major pathogen of cattle, with severe infections being fatal. In this study, we provide first insights into the transcriptome of the adult stage of D. viviparus through the analysis of expressed sequence tags (ESTs).

Results: Using our EST analysis pipeline, we estimate that the present dataset of 4436 ESTs is derived from 2258 genes based on cluster and comparative genomic analyses of the ESTs. Of the 2258 representative ESTs, 1159 (51.3%) had homologues in the free-living nematode C. elegans, 1174 (51.9%) in parasitic nematodes, 827 (36.6%) in organisms other than nematodes, and 863 (38%) had no significant match to any sequence in the current databases. Of the C. elegans homologues, 569 had observed 'non-wildtype' RNAi phenotypes, including embryonic lethality, maternal sterility, sterility in progeny, larval arrest and slow growth. We could functionally classify 776 (35%) sequences using the Gene Ontologies (GO) and established pathway associations to 696 (31%) sequences in Kyoto Encyclopedia of Genes and Genomes (KEGG). In addition, we predicted 85 secreted proteins which could represent potential candidates for developing novel anthelmintics or vaccines.

Conclusion: The bioinformatic analyses of ESTs data for D. viviparus has elucidated sets of relatively conserved and potentially novel genes. The genes discovered in this study should assist research toward a better understanding of the basic molecular biology of D. viviparus, which could lead, in the longer term, to novel intervention strategies. The characterization of the D. viviparus transcriptome also provides a foundation for whole genome sequence analysis and future comparative transcriptomic analyses.

Show MeSH
Related in: MedlinePlus