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

Siewert C, Hess WR, Duduk B, Huettel B, Reinhardt R, Büttner C, Kube M - BMC Genomics (2014)

Bottom Line: Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence.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 F1FO-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.

View Article: PubMed Central - PubMed

Affiliation: Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute, Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany. Michael.Kube@agrar.hu-berlin.de.

ABSTRACT

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 F1FO-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 F1FO-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.

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An overview of the subunits of the F- and V-type ATPases encoded by acholeplasma genomes. The subunit order follows location within the chromosomes. Genes shared by all of the four acholeplasmas are highlighted in blue. Numbers indicate locus tags corresponding to the deduced proteins.
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Fig8: An overview of the subunits of the F- and V-type ATPases encoded by acholeplasma genomes. The subunit order follows location within the chromosomes. Genes shared by all of the four acholeplasmas are highlighted in blue. Numbers indicate locus tags corresponding to the deduced proteins.

Mentions: Beside GroEL/ES, A. oculi lacks the complete gene set encoding the F1FO-type Na+ ATPase, which was identified in A. laidlawii, A. brassicae and A. palmae (Figures 8 and 9). Therefore, A. oculi, A. laidlawii and A. palmae encode one V-type Na+ ATPase. A. palmae differs in gene content by encoding no atpC subunit for this ATPase. In addition, all genes encoding the V1VO H+ ATPase are present in all four acholeplasma strains. Summing up, each acholeplasma species possesses at least one full operon which encodes at least either one H+ or one Na+ ATPase system. The NtpG subunit, namely the rotated central stalk next to NtpD and NtpC [35], is missing in all species. In contrast to the acholeplasmas, the F- and V-type ATPases were not identified in phytoplasmas.Figure 8


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

Siewert C, Hess WR, Duduk B, Huettel B, Reinhardt R, Büttner C, Kube M - BMC Genomics (2014)

An overview of the subunits of the F- and V-type ATPases encoded by acholeplasma genomes. The subunit order follows location within the chromosomes. Genes shared by all of the four acholeplasmas are highlighted in blue. Numbers indicate locus tags corresponding to the deduced proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4221730&req=5

Fig8: An overview of the subunits of the F- and V-type ATPases encoded by acholeplasma genomes. The subunit order follows location within the chromosomes. Genes shared by all of the four acholeplasmas are highlighted in blue. Numbers indicate locus tags corresponding to the deduced proteins.
Mentions: Beside GroEL/ES, A. oculi lacks the complete gene set encoding the F1FO-type Na+ ATPase, which was identified in A. laidlawii, A. brassicae and A. palmae (Figures 8 and 9). Therefore, A. oculi, A. laidlawii and A. palmae encode one V-type Na+ ATPase. A. palmae differs in gene content by encoding no atpC subunit for this ATPase. In addition, all genes encoding the V1VO H+ ATPase are present in all four acholeplasma strains. Summing up, each acholeplasma species possesses at least one full operon which encodes at least either one H+ or one Na+ ATPase system. The NtpG subunit, namely the rotated central stalk next to NtpD and NtpC [35], is missing in all species. In contrast to the acholeplasmas, the F- and V-type ATPases were not identified in phytoplasmas.Figure 8

Bottom Line: Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence.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 F1FO-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.

View Article: PubMed Central - PubMed

Affiliation: Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute, Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany. Michael.Kube@agrar.hu-berlin.de.

ABSTRACT

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 F1FO-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 F1FO-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.

Show MeSH
Related in: MedlinePlus