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The Mycoplasma conjunctivae genome sequencing, annotation and analysis.

Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L - BMC Bioinformatics (2009)

Bottom Line: Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death.This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).The resulting annotations are stored in a MySQL database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Swiss Institute of Bioinformatics, Génopode-UNIL, 1015 Lausanne, Switzerland. Sandra.Calderon@unil.ch

ABSTRACT

Background: The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).

Methods: The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database.

Results: The annotated sequence is deposited in the EMBL database (FM864216) and uploaded into the mollicutes database MolliGen http://cbi.labri.fr/outils/molligen/ allowing for comparative genomics.

Conclusion: We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).

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Related in: MedlinePlus

Origin of replication. The region between rpmH and dnaA genes for the 3 M. hyopneumoniae strains aligned with M. conjunctivae. The two putative dnaA boxes are shown in black. M. hyopneumoniae J (NC_007295), M. hyopneumoniae 7448 (NC_007332), M. hyopneumoniae 232 (NC_006360), M. conjunctivae (FM864216).
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Figure 2: Origin of replication. The region between rpmH and dnaA genes for the 3 M. hyopneumoniae strains aligned with M. conjunctivae. The two putative dnaA boxes are shown in black. M. hyopneumoniae J (NC_007295), M. hyopneumoniae 7448 (NC_007332), M. hyopneumoniae 232 (NC_006360), M. conjunctivae (FM864216).

Mentions: The origin of replication (oriC) was searched by comparing the sequences of 3 strains of M. hyopneumoniae with the sequence of M. conjunctivae in the region of dnaA gene (Figure 2). We attempted to identify several features that have been associated with replication origins in other bacterial species, including mollicutes. Bacterial origins of replication are typically located in the vicinity of the dnaA and dnaN genes. Usually several dnaA-box motifs are found within the intergenic regions around dnaA gene [26]. We searched unsuccessfully for the presence of consensus dnaA-box motifs with the pattern TTATC [CA]A [CA] using fuzznuc of the EMBOSS package [27]. When we used a slightly different, more relaxed dnaA-box consensus motifs TT [AT] [AC] [ACT]A [AC]A, two sequences matching each of these patterns were found between the dnaA and rpmH genes (Figure 2). However, well over 3,000 hits located throughout the rest of the genome were also seen. Therefore, the specificity of the pattern used to try to detect dnaA-box motifs was very low, decreasing our confidence in the significance of the sequences identified.


The Mycoplasma conjunctivae genome sequencing, annotation and analysis.

Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L - BMC Bioinformatics (2009)

Origin of replication. The region between rpmH and dnaA genes for the 3 M. hyopneumoniae strains aligned with M. conjunctivae. The two putative dnaA boxes are shown in black. M. hyopneumoniae J (NC_007295), M. hyopneumoniae 7448 (NC_007332), M. hyopneumoniae 232 (NC_006360), M. conjunctivae (FM864216).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697654&req=5

Figure 2: Origin of replication. The region between rpmH and dnaA genes for the 3 M. hyopneumoniae strains aligned with M. conjunctivae. The two putative dnaA boxes are shown in black. M. hyopneumoniae J (NC_007295), M. hyopneumoniae 7448 (NC_007332), M. hyopneumoniae 232 (NC_006360), M. conjunctivae (FM864216).
Mentions: The origin of replication (oriC) was searched by comparing the sequences of 3 strains of M. hyopneumoniae with the sequence of M. conjunctivae in the region of dnaA gene (Figure 2). We attempted to identify several features that have been associated with replication origins in other bacterial species, including mollicutes. Bacterial origins of replication are typically located in the vicinity of the dnaA and dnaN genes. Usually several dnaA-box motifs are found within the intergenic regions around dnaA gene [26]. We searched unsuccessfully for the presence of consensus dnaA-box motifs with the pattern TTATC [CA]A [CA] using fuzznuc of the EMBOSS package [27]. When we used a slightly different, more relaxed dnaA-box consensus motifs TT [AT] [AC] [ACT]A [AC]A, two sequences matching each of these patterns were found between the dnaA and rpmH genes (Figure 2). However, well over 3,000 hits located throughout the rest of the genome were also seen. Therefore, the specificity of the pattern used to try to detect dnaA-box motifs was very low, decreasing our confidence in the significance of the sequences identified.

Bottom Line: Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death.This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).The resulting annotations are stored in a MySQL database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Swiss Institute of Bioinformatics, Génopode-UNIL, 1015 Lausanne, Switzerland. Sandra.Calderon@unil.ch

ABSTRACT

Background: The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).

Methods: The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database.

Results: The annotated sequence is deposited in the EMBL database (FM864216) and uploaded into the mollicutes database MolliGen http://cbi.labri.fr/outils/molligen/ allowing for comparative genomics.

Conclusion: We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).

Show MeSH
Related in: MedlinePlus