Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture

BMC Genomics

Renaud Maillard¹  Nadia Haddad²  Henri-Jean Boulouis²  Anne-Claire Lagrée²  Marco Moroldo³  Sylvain Marthey³  Valentin Loux⁴  Thibaud Dugat² 

[1] Unité pathologie des ruminants, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France;Université Paris-Est, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France;INRA, Centre de Ressources Biologiques Génomique des Animaux Domestiques et d’Intérêt Economique, Jouy-En-Josas, France;INRA, UR1077 Mathématique, Informatique et Génome, Jouy-En-Josas, France

关键词: Whole genome sequencing;    Targeted sequence capture;    Tick-borne fever;    Granulocytic anaplasmosis;    Comparative genomics;    Cattle;    Anaplasma phagocytophilum;   

Others  :  1127600
DOI  :  10.1186/1471-2164-15-973

 received in 2014-08-13, accepted in 2014-10-30,  发布年份 2014

【 摘 要 】

Background

Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.

Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains.

Results

DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function” and require further analysis. We also identified nine proteins common to both European domestic ruminants tested.

Conclusion

Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored.

【 授权许可】

   
2014 Dugat et al.; licensee BioMed Central Ltd.

【 图 表 】

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