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Haloquadratum walsbyi: limited diversity in a global pond.

Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D - PLoS ONE (2011)

Bottom Line: Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species.The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

View Article: PubMed Central - PubMed

Affiliation: Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. mdyall-smith@csu.edu.au

ABSTRACT

Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.

Principal findings: Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.

Conclusions: Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

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Categories of strain-specific regions, plotted according to the relative numbers in each type.Pie chart showing the types of strain specific regions in both strains. Blue: mobile genetic elements, which includes transposons and transposase-free mobile elements (MITEs, PATEs, and SMRs). Green: insertions and deletions (indels). Red: Deletion-Coupled Insertions (DCI). Long indels and DCIs (> 1.5 kb) are filled colour sectors while medium (0.15–1.5 kb) or short (20–150 bp) sequences in these categories are dotted. Numbers at the outer edge of each sector are the numbers of cases in each category. Data from Table S4.
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pone-0020968-g006: Categories of strain-specific regions, plotted according to the relative numbers in each type.Pie chart showing the types of strain specific regions in both strains. Blue: mobile genetic elements, which includes transposons and transposase-free mobile elements (MITEs, PATEs, and SMRs). Green: insertions and deletions (indels). Red: Deletion-Coupled Insertions (DCI). Long indels and DCIs (> 1.5 kb) are filled colour sectors while medium (0.15–1.5 kb) or short (20–150 bp) sequences in these categories are dotted. Numbers at the outer edge of each sector are the numbers of cases in each category. Data from Table S4.

Mentions: Each of the 360 strain-specific sequences represents some type of insertion or deletion (indel), which could be classified into one of several categories (Figure 6, Table S4). About half of the indels represent mobile genetic elements (see below) while the other half are unrelated to known mobile genetic elements. The smallest indels are just longer than 20 bp (the lower cut-off size for manual inspection) while the largest is more than 100 kb (in DV12). Some of the short indels were sub-classified as “polyrepeats”, and consist of a short (e.g. 6-mer) repeated sequence (allowing for some variability), where the number of copies differs between the two strains. For polyrepeats, an exact point of insertion/deletion cannot be defined. Several polyrepeat indels are located within coding regions, where the proteins from the two strains have e.g. dipeptide repeats of different length but with the reading frame conserved.


Haloquadratum walsbyi: limited diversity in a global pond.

Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D - PLoS ONE (2011)

Categories of strain-specific regions, plotted according to the relative numbers in each type.Pie chart showing the types of strain specific regions in both strains. Blue: mobile genetic elements, which includes transposons and transposase-free mobile elements (MITEs, PATEs, and SMRs). Green: insertions and deletions (indels). Red: Deletion-Coupled Insertions (DCI). Long indels and DCIs (> 1.5 kb) are filled colour sectors while medium (0.15–1.5 kb) or short (20–150 bp) sequences in these categories are dotted. Numbers at the outer edge of each sector are the numbers of cases in each category. Data from Table S4.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3119063&req=5

pone-0020968-g006: Categories of strain-specific regions, plotted according to the relative numbers in each type.Pie chart showing the types of strain specific regions in both strains. Blue: mobile genetic elements, which includes transposons and transposase-free mobile elements (MITEs, PATEs, and SMRs). Green: insertions and deletions (indels). Red: Deletion-Coupled Insertions (DCI). Long indels and DCIs (> 1.5 kb) are filled colour sectors while medium (0.15–1.5 kb) or short (20–150 bp) sequences in these categories are dotted. Numbers at the outer edge of each sector are the numbers of cases in each category. Data from Table S4.
Mentions: Each of the 360 strain-specific sequences represents some type of insertion or deletion (indel), which could be classified into one of several categories (Figure 6, Table S4). About half of the indels represent mobile genetic elements (see below) while the other half are unrelated to known mobile genetic elements. The smallest indels are just longer than 20 bp (the lower cut-off size for manual inspection) while the largest is more than 100 kb (in DV12). Some of the short indels were sub-classified as “polyrepeats”, and consist of a short (e.g. 6-mer) repeated sequence (allowing for some variability), where the number of copies differs between the two strains. For polyrepeats, an exact point of insertion/deletion cannot be defined. Several polyrepeat indels are located within coding regions, where the proteins from the two strains have e.g. dipeptide repeats of different length but with the reading frame conserved.

Bottom Line: Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species.The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

View Article: PubMed Central - PubMed

Affiliation: Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. mdyall-smith@csu.edu.au

ABSTRACT

Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.

Principal findings: Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.

Conclusions: Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

Show MeSH
Related in: MedlinePlus