Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae

BMC Genomics

Michael Kube¹  Carmen Büttner¹  Richard Reinhardt²  Bruno Huettel²  Bojan Duduk³  Wolfgang R Hess⁴  Christin Siewert¹ 

[1] Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute, Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany;Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;Institute of Pesticides and Environmental Protection, Banatska 31b, P.O. Box 163, 11080 Belgrade, Serbia;Genetics & Experimental Bioinformatics, University of Freiburg, Institute of Biology III, Schänzlestraße 1, 79104 Freiburg, Germany

Others  :  1128426
DOI  :  10.1186/1471-2164-15-931

 received in 2014-06-04, accepted in 2014-09-25,  发布年份 2014

【 摘 要 】

Background

Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera Acholeplasma and ‘Candidatus Phytoplasma’. Acholeplasmas are ubiquitous saprophytic bacteria. Several isolates are derived from plants or animals, whereas phytoplasmas are characterised as intracellular parasitic pathogens of plant phloem and depend on insect vectors for their spread. The complete genome sequences for eight strains of this family have been resolved so far, all of which were determined depending on clone-based sequencing.

Results

The A. oculi strain 19L chromosome was sequenced using two independent approaches. The first approach comprised sequencing by synthesis (Illumina) in combination with Sanger sequencing, while single molecule real time sequencing (PacBio) was used in the second. The genome was determined to be 1,587,120 bp in size. Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence. High-quality sequences were obtained by both strategies differing in six positions, which are interpreted as reliable variations present in the culture population. Our genome analysis revealed 1,471 protein-coding genes and highlighted the absence of the F₁F_O-type Na⁺ ATPase system and GroEL/ES chaperone. Comparison of the four available Acholeplasma sequences revealed a core-genome encoding 703 proteins and a pan-genome of 2,867 proteins.

Conclusions

The application of two state-of-the-art sequencing technologies highlights the potential of single molecule real time sequencing for complete genome determination. Comparative genome analyses revealed that the process of losing particular basic genetic features during genome reduction occurs in both genera, as indicated for several phytoplasma strains and at least A. oculi. The loss of the F₁F_O-type Na⁺ ATPase system may separate Acholeplasmataceae from other Mollicutes, while the loss of those genes encoding the chaperone GroEL/ES is not a rare exception in this bacterial class.

【 授权许可】

   
2014 Siewert et al.; licensee BioMed Central Ltd.

【 图 表 】

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