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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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Locus tags of the encoded chaperons and heat shock proteins within theAcholeplasmataceae. Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, ACL; A. palmae, Apal; A. brassicae, Abra; ‘Candidatus P. mali’ strain AT, ATP; ‘Ca. P. australiense’ strain rp-A, PA; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M, PAM; ‘Ca. P. asteris’ strain AY-WB, AYWB. Shared proteins are highlighted in blue.
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Fig7: Locus tags of the encoded chaperons and heat shock proteins within theAcholeplasmataceae. Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, ACL; A. palmae, Apal; A. brassicae, Abra; ‘Candidatus P. mali’ strain AT, ATP; ‘Ca. P. australiense’ strain rp-A, PA; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M, PAM; ‘Ca. P. asteris’ strain AY-WB, AYWB. Shared proteins are highlighted in blue.

Mentions: All species of the Acholeplasmataceae encode a protein core for the Sec-dependent secretion system (Ffh, FtsY, SecA, SecE, SecY and YidC), whereas the four analysed Acholeplasma spp. additionally encode the membrane protein SecG. The chaperone SecB, which is only encoded in A. laidlawii and A. oculi, binds the precursor protein and directs it to the SecA protein. The function of SecB can also be fulfilled by the proteins DnaK and DnaJ [31], which are encoded in all genome sequences of the family, or by GroEL and GroES [32]. A. oculi lacks the common chaperone GroEL/ES (Figure 7), consistent with conclusions drawn from the draft sequences of phytoplasma strains [33] and the analyses of other species in the Mollicutes that these genes are not essential [34]. The complete genome sequences of the Acholeplasmataceae encode the trigger factor (TF), dnaK, dnaJ, grpE and hrcA. Other heat shock proteins, such as Hsp20, were not identified in A. palmae and ‘Ca. P. mali’. Hsp33 is only identified in the acholeplasmas.Figure 7


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)

Locus tags of the encoded chaperons and heat shock proteins within theAcholeplasmataceae. Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, ACL; A. palmae, Apal; A. brassicae, Abra; ‘Candidatus P. mali’ strain AT, ATP; ‘Ca. P. australiense’ strain rp-A, PA; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M, PAM; ‘Ca. P. asteris’ strain AY-WB, AYWB. Shared proteins are highlighted in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Locus tags of the encoded chaperons and heat shock proteins within theAcholeplasmataceae. Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, ACL; A. palmae, Apal; A. brassicae, Abra; ‘Candidatus P. mali’ strain AT, ATP; ‘Ca. P. australiense’ strain rp-A, PA; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M, PAM; ‘Ca. P. asteris’ strain AY-WB, AYWB. Shared proteins are highlighted in blue.
Mentions: All species of the Acholeplasmataceae encode a protein core for the Sec-dependent secretion system (Ffh, FtsY, SecA, SecE, SecY and YidC), whereas the four analysed Acholeplasma spp. additionally encode the membrane protein SecG. The chaperone SecB, which is only encoded in A. laidlawii and A. oculi, binds the precursor protein and directs it to the SecA protein. The function of SecB can also be fulfilled by the proteins DnaK and DnaJ [31], which are encoded in all genome sequences of the family, or by GroEL and GroES [32]. A. oculi lacks the common chaperone GroEL/ES (Figure 7), consistent with conclusions drawn from the draft sequences of phytoplasma strains [33] and the analyses of other species in the Mollicutes that these genes are not essential [34]. The complete genome sequences of the Acholeplasmataceae encode the trigger factor (TF), dnaK, dnaJ, grpE and hrcA. Other heat shock proteins, such as Hsp20, were not identified in A. palmae and ‘Ca. P. mali’. Hsp33 is only identified in the acholeplasmas.Figure 7

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