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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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SimiTri profile of predicted R. microplus genes. The predicted protein-coding region for each R. microplus TC or singleton was searched against the protein databases for whole genomes (a-c) using BlastP or tick EST databases (d) using TBlastN (E value < 1 × 10-8). Three translated databases are selected for comparison in each profile. The position for each tile represents its similarity to the hits in each different genome as calculated by Blast search raw scores. The color is coded based on the highest Blast score as: red > 300; yellow > 200; green > 150; blue > 100 and purple < 100.
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Figure 1: SimiTri profile of predicted R. microplus genes. The predicted protein-coding region for each R. microplus TC or singleton was searched against the protein databases for whole genomes (a-c) using BlastP or tick EST databases (d) using TBlastN (E value < 1 × 10-8). Three translated databases are selected for comparison in each profile. The position for each tile represents its similarity to the hits in each different genome as calculated by Blast search raw scores. The color is coded based on the highest Blast score as: red > 300; yellow > 200; green > 150; blue > 100 and purple < 100.

Mentions: Positional clustering reveals the relationship between genes from R. microplus and those from the queried genomes. Additionally, genes which locate along an edge of the triangle have no significant match to the database represented on the opposing vertex of the triangle. Using the conceptually translated sequences of BmiGI, the R. microplus data was compared with combinations of data derived from the genome sequences of four other metazoans (H. sapiens, D. melanogaster, C. elegans, and A. gambiae) and the unicellular organism S. cerevisiae (Figure 1). When compared with S. cerevisiae, D. melanogaster and H. sapiens (Figure 1a), the tick's sequences group closer to D. melanogaster than the other two organisms, with the tick appearing most distant from S. cerevisiae, an expected result since S. cerevisiae is a unicellular organism. Although both R. microplus and D. melanogaster are arthropods, some R. microplus genes appear to be more similar to human genes than D. melanogaster as evidenced in Figure 1a. Genes with these atypical gene similarities were selected for more detailed examination of their Blast results and will be discussed later. Upon replacement of S. cerevisiae with C. elegans (Figure 1b), most of the predicted relationships appear clustered near the center, but careful examination shows slightly greater clustering toward the D. melanogaster genome than C. elegans or H. sapiens. Replacement of C. elegans with A. gambiae resulted in a roughly symmetrical alignment between D. melanogaster and A. gambiae, although some atypical genes cluster near H. sapiens (Figure 1c). Finally, when the R. microplus genes were compared with the three tick EST databases, R. appendiculatus, I. scapularis, and A. variegatum, most genes are clustered closer to R. appendiculatus than the other two ticks (Figure 1d). This result is consistent with the phylogenetic classifications of these 4 species of ticks [21].


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

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

SimiTri profile of predicted R. microplus genes. The predicted protein-coding region for each R. microplus TC or singleton was searched against the protein databases for whole genomes (a-c) using BlastP or tick EST databases (d) using TBlastN (E value < 1 × 10-8). Three translated databases are selected for comparison in each profile. The position for each tile represents its similarity to the hits in each different genome as calculated by Blast search raw scores. The color is coded based on the highest Blast score as: red > 300; yellow > 200; green > 150; blue > 100 and purple < 100.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: SimiTri profile of predicted R. microplus genes. The predicted protein-coding region for each R. microplus TC or singleton was searched against the protein databases for whole genomes (a-c) using BlastP or tick EST databases (d) using TBlastN (E value < 1 × 10-8). Three translated databases are selected for comparison in each profile. The position for each tile represents its similarity to the hits in each different genome as calculated by Blast search raw scores. The color is coded based on the highest Blast score as: red > 300; yellow > 200; green > 150; blue > 100 and purple < 100.
Mentions: Positional clustering reveals the relationship between genes from R. microplus and those from the queried genomes. Additionally, genes which locate along an edge of the triangle have no significant match to the database represented on the opposing vertex of the triangle. Using the conceptually translated sequences of BmiGI, the R. microplus data was compared with combinations of data derived from the genome sequences of four other metazoans (H. sapiens, D. melanogaster, C. elegans, and A. gambiae) and the unicellular organism S. cerevisiae (Figure 1). When compared with S. cerevisiae, D. melanogaster and H. sapiens (Figure 1a), the tick's sequences group closer to D. melanogaster than the other two organisms, with the tick appearing most distant from S. cerevisiae, an expected result since S. cerevisiae is a unicellular organism. Although both R. microplus and D. melanogaster are arthropods, some R. microplus genes appear to be more similar to human genes than D. melanogaster as evidenced in Figure 1a. Genes with these atypical gene similarities were selected for more detailed examination of their Blast results and will be discussed later. Upon replacement of S. cerevisiae with C. elegans (Figure 1b), most of the predicted relationships appear clustered near the center, but careful examination shows slightly greater clustering toward the D. melanogaster genome than C. elegans or H. sapiens. Replacement of C. elegans with A. gambiae resulted in a roughly symmetrical alignment between D. melanogaster and A. gambiae, although some atypical genes cluster near H. sapiens (Figure 1c). Finally, when the R. microplus genes were compared with the three tick EST databases, R. appendiculatus, I. scapularis, and A. variegatum, most genes are clustered closer to R. appendiculatus than the other two ticks (Figure 1d). This result is consistent with the phylogenetic classifications of these 4 species of ticks [21].

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