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Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus.

Wang M, Guerrero FD, Pertea G, Nene VM - BMC Genomics (2007)

Bottom Line: Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks.These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes.This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lorus Therapeutics Inc; 2 Meridian Road, Toronto, ON M9W 4Z7, Canada. Minghua.Wang@yahoo.com

ABSTRACT

Background: The southern cattle tick, Rhipicephalus (Boophilus) microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks.

Results: We present a global comparative genomic analysis of a gene index of R. microplus comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs), a significant fraction of the complement of R. microplus genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of R. microplus, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology.

Conclusion: These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes. Members of this group would likely be poor choices as targets for development of novel tick control technology.

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Phylogenetic tree analysis of atypical genes from SimiTri analysis. The atypically clustering genes circled in Figure 1a-c were analyzed by BlastP analysis and phylogenetic trees generated with outputs scaled to show distance between sequences. The BmiGI entries were TC14523 (a), TC9268 (b), TC13445 (c) and TC12600 (d) and the TC query sequence is noted in the figure as Rhipicephalus microplus in bold underlined text. The alignments used to generate the trees are included as Additional files 2, 4, 6, 8 in text format. The entire tree is included in pdf file format as Additional files 1, 3, 5, and 7 and only subtrees showing the nearest related sequences are included here.
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Figure 2: Phylogenetic tree analysis of atypical genes from SimiTri analysis. The atypically clustering genes circled in Figure 1a-c were analyzed by BlastP analysis and phylogenetic trees generated with outputs scaled to show distance between sequences. The BmiGI entries were TC14523 (a), TC9268 (b), TC13445 (c) and TC12600 (d) and the TC query sequence is noted in the figure as Rhipicephalus microplus in bold underlined text. The alignments used to generate the trees are included as Additional files 2, 4, 6, 8 in text format. The entire tree is included in pdf file format as Additional files 1, 3, 5, and 7 and only subtrees showing the nearest related sequences are included here.

Mentions: Phylogenetically, ticks and insects belong to the arthropod phylum and would be expected to share more gene similarity than genes from ticks and mammals. However, SimiTri analysis revealed some atypical genes which were observed to cluster closer to human genes than either D. melanogaster or A. gambiae genes. The three most atypical genes are circled in Figure 1a–c and listed in Table 2. TC14523 contains the closest similarity to human genes in all the three comparisons of Figure 1a–c. The top Blast hit for TC14523 is Dusty protein kinase (E-Value = 1 × 10-138), a protein with a dual functional kinase domain, whose specific biological role has not yet been identified. While most databases classify this protein as a receptor interacting kinase, detailed analysis demonstrated that this is a single copy unique kinase which seems to be present in all vertebrates [22]. An EST [GenBank:CD782617.1] from R. appendiculatus, a three host tick parasitizing livestock, shows 91% nucleotide identity to TC14523. Thus, at least two ticks possess this gene and it would be very interesting to know the function of this gene in humans and ticks. Perhaps the function would reveal why the atypical sequence similarity exists for this gene of R. microplus. To further investigate the relationship of TC14523 to other Dusty protein kinases with a more powerful method of phylogenetic analysis, we performed a BlastP and Clustal analysis of the conceptual coding region of TC14523 followed by generation of the corresponding phylogenetic tree. Figure 2a shows the coding region of TC14523 is most closely related a Dusty protein kinase from sea urchin with similarities to several Dusty protein kinases from various aquatic species and mammals. In fact, other than two Dusty protein kinases from Apis mellifera, arthropod insect sequences seem to be absent from the tree of close relatives to the R. microplus sequence (Figure 2a, Additional files 1 and 2). Perhaps this gene has been lost from most insects and the absence of this gene from dipterans would explain why TC14523 clustered near H. sapiens in the SimiTri analysis of Figure 1a–c.


Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus.

Wang M, Guerrero FD, Pertea G, Nene VM - BMC Genomics (2007)

Phylogenetic tree analysis of atypical genes from SimiTri analysis. The atypically clustering genes circled in Figure 1a-c were analyzed by BlastP analysis and phylogenetic trees generated with outputs scaled to show distance between sequences. The BmiGI entries were TC14523 (a), TC9268 (b), TC13445 (c) and TC12600 (d) and the TC query sequence is noted in the figure as Rhipicephalus microplus in bold underlined text. The alignments used to generate the trees are included as Additional files 2, 4, 6, 8 in text format. The entire tree is included in pdf file format as Additional files 1, 3, 5, and 7 and only subtrees showing the nearest related sequences are included here.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2100071&req=5

Figure 2: Phylogenetic tree analysis of atypical genes from SimiTri analysis. The atypically clustering genes circled in Figure 1a-c were analyzed by BlastP analysis and phylogenetic trees generated with outputs scaled to show distance between sequences. The BmiGI entries were TC14523 (a), TC9268 (b), TC13445 (c) and TC12600 (d) and the TC query sequence is noted in the figure as Rhipicephalus microplus in bold underlined text. The alignments used to generate the trees are included as Additional files 2, 4, 6, 8 in text format. The entire tree is included in pdf file format as Additional files 1, 3, 5, and 7 and only subtrees showing the nearest related sequences are included here.
Mentions: Phylogenetically, ticks and insects belong to the arthropod phylum and would be expected to share more gene similarity than genes from ticks and mammals. However, SimiTri analysis revealed some atypical genes which were observed to cluster closer to human genes than either D. melanogaster or A. gambiae genes. The three most atypical genes are circled in Figure 1a–c and listed in Table 2. TC14523 contains the closest similarity to human genes in all the three comparisons of Figure 1a–c. The top Blast hit for TC14523 is Dusty protein kinase (E-Value = 1 × 10-138), a protein with a dual functional kinase domain, whose specific biological role has not yet been identified. While most databases classify this protein as a receptor interacting kinase, detailed analysis demonstrated that this is a single copy unique kinase which seems to be present in all vertebrates [22]. An EST [GenBank:CD782617.1] from R. appendiculatus, a three host tick parasitizing livestock, shows 91% nucleotide identity to TC14523. Thus, at least two ticks possess this gene and it would be very interesting to know the function of this gene in humans and ticks. Perhaps the function would reveal why the atypical sequence similarity exists for this gene of R. microplus. To further investigate the relationship of TC14523 to other Dusty protein kinases with a more powerful method of phylogenetic analysis, we performed a BlastP and Clustal analysis of the conceptual coding region of TC14523 followed by generation of the corresponding phylogenetic tree. Figure 2a shows the coding region of TC14523 is most closely related a Dusty protein kinase from sea urchin with similarities to several Dusty protein kinases from various aquatic species and mammals. In fact, other than two Dusty protein kinases from Apis mellifera, arthropod insect sequences seem to be absent from the tree of close relatives to the R. microplus sequence (Figure 2a, Additional files 1 and 2). Perhaps this gene has been lost from most insects and the absence of this gene from dipterans would explain why TC14523 clustered near H. sapiens in the SimiTri analysis of Figure 1a–c.

Bottom Line: Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks.These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes.This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lorus Therapeutics Inc; 2 Meridian Road, Toronto, ON M9W 4Z7, Canada. Minghua.Wang@yahoo.com

ABSTRACT

Background: The southern cattle tick, Rhipicephalus (Boophilus) microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks.

Results: We present a global comparative genomic analysis of a gene index of R. microplus comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs), a significant fraction of the complement of R. microplus genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of R. microplus, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology.

Conclusion: These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes. Members of this group would likely be poor choices as targets for development of novel tick control technology.

Show MeSH
Related in: MedlinePlus