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Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.

Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT - PLoS Genet. (2014)

Bottom Line: We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain.The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation.Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Graduate Group, University of California, Davis, Davis, California, United States of America; Genome Center, University of California, Davis, Davis, California, United States of America.

ABSTRACT
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

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Sequencing depth of newly sequenced haloarchaeal genomes.Histogram showing distribution of mean per base coverage for the 59 newly-sequenced and seven previously published draft genomes [109] included in this study.
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pgen-1004784-g001: Sequencing depth of newly sequenced haloarchaeal genomes.Histogram showing distribution of mean per base coverage for the 59 newly-sequenced and seven previously published draft genomes [109] included in this study.

Mentions: Fifty-nine haloarchaeal isolates from 17 genera were sequenced on Illumina GAII and HiSeq platforms using a combination of paired-end (85 nt reads), mate-pair (6 Kbp fragments), PCR-free paired-end, and unbarcoded “SOUP” libraries. SOUP libraries were prepared by pooling unbarcoded libraries for several species, which were phylogenetically distant enough to enable unambiguous read mapping. For library preparation details, see Materials and Methods; for information on methods used for each genome, see Table S2. Mean per base sequencing depth ranged from 13x to 188x, with a mean coverage of 90x (Figure 1). Sequence reads were assembled into contigs using the a5 pipeline [18], with a cross-species mean of 75 and median of 66 contigs. Genome assemblies ranged from 3.06 to 4.94 Mbp in size and all demonstrated high G+C content (mean of 62%) and high coding density (mean of 82%), as expected. Contig assemblies have been deposited in the NCBI genomic database along with annotations derived from the Prokaryotic Genome Annotation Pipeline (PGAAP) [14]. This annotation pipeline called between 2,945 and 4,645 putative protein coding regions, depending on the species.


Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.

Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT - PLoS Genet. (2014)

Sequencing depth of newly sequenced haloarchaeal genomes.Histogram showing distribution of mean per base coverage for the 59 newly-sequenced and seven previously published draft genomes [109] included in this study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230888&req=5

pgen-1004784-g001: Sequencing depth of newly sequenced haloarchaeal genomes.Histogram showing distribution of mean per base coverage for the 59 newly-sequenced and seven previously published draft genomes [109] included in this study.
Mentions: Fifty-nine haloarchaeal isolates from 17 genera were sequenced on Illumina GAII and HiSeq platforms using a combination of paired-end (85 nt reads), mate-pair (6 Kbp fragments), PCR-free paired-end, and unbarcoded “SOUP” libraries. SOUP libraries were prepared by pooling unbarcoded libraries for several species, which were phylogenetically distant enough to enable unambiguous read mapping. For library preparation details, see Materials and Methods; for information on methods used for each genome, see Table S2. Mean per base sequencing depth ranged from 13x to 188x, with a mean coverage of 90x (Figure 1). Sequence reads were assembled into contigs using the a5 pipeline [18], with a cross-species mean of 75 and median of 66 contigs. Genome assemblies ranged from 3.06 to 4.94 Mbp in size and all demonstrated high G+C content (mean of 62%) and high coding density (mean of 82%), as expected. Contig assemblies have been deposited in the NCBI genomic database along with annotations derived from the Prokaryotic Genome Annotation Pipeline (PGAAP) [14]. This annotation pipeline called between 2,945 and 4,645 putative protein coding regions, depending on the species.

Bottom Line: We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain.The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation.Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Graduate Group, University of California, Davis, Davis, California, United States of America; Genome Center, University of California, Davis, Davis, California, United States of America.

ABSTRACT
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

Show MeSH
Related in: MedlinePlus