Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Cassier‐Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

doi:10.3389/fmicb.2016.01809

Cited by 67 publications

(68 citation statements)

References 110 publications

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“…A linear regression model is shown (F-statistic: 11.9, Adjusted R-squared: 0.38, p = 0.003). three functional domains [60], and identified loci with additional genes involved in DNA uptake and recombination [61] (Supplementary Table S3). We found that the presence of a ComEC homolog with multiple adjacent operonic recombination-related genes was strongly associated with the lowest values of D' (Fig.…”

Section: Homologous Recombination Is Common But Populations Exist Famentioning

confidence: 99%

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

et al. 2020

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Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.

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Section: Homologous Recombination Is Common But Populations Exist Famentioning

confidence: 99%

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

et al. 2020

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“…Given evidence for recent homologous recombination, we searched the genomes for genes that could confer natural competence, such as homologs of the ComEC gene with all three functional domains (Pimentel and Zhang 2018), and identified loci with additional genes involved in DNA uptake and recombination (Cassier-Chauvat et al 2016) ( Supplementary Table S3 ). We found that presence of a ComEC homolog with multiple adjacent operonic recombination-related genes was strongly associated with the lowest values of D’ ( Fig 4d ).…”

Section: Resultsmentioning

confidence: 99%

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

Crits-Christoph

Olm

Diamond

et al. 2019

Preprint

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Soil microbial diversity is often studied from the perspective of community 12 composition, but less is known about genetic heterogeneity within species and how population 13 structures are affected by dispersal, recombination, and selection. Genomic inferences about 14 population structure can be made using the millions of sequencing reads that are assembled de 15 novo into consensus genomes from metagenomes, as each read pair describes a short genomic 16 sequence from a cell in the population. Here we track genome-wide population genetic variation 17 for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic 18 nucleotide identity of assembled genomes was significantly associated with local geography for 19 half of the populations studied, and for a majority of populations within-sample nucleotide 20 diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in specialized 21 metabolite biosynthesis and extracellular transport were characterized by elevated genetic diversity 22 in multiple species. Microbial populations displayed varying degrees of homologous recombination 23 and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple 24 populations we identified genes with unusually high site-specific differentiation of alleles, fewer 25 recombinant events, and lower nucleotide diversity, suggesting recent selective sweeps for gene 26 variants. Taken together, these results indicate that recombination and gene-specific selection 27 commonly shape local soil bacterial genetic variation. 28 29 31

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“…PCC 7002, Thermosynechococcus elongatus BP-1, Microcystis aeruginosa PCC 7806 and, Phormidium lacuna HE10JO (8-13). The strains Phormidium lacuna HE10JO and HE10DO are very similar and the genomic data for HE10JO is considered also relevant for the strain HE10DO (31). This set of proteins is used to define a range of similarity to decide whether other homologs are functional or not.…”

Section: Resultsmentioning

confidence: 99%

“…Segregation into the other chromosomes can be achieved by selection on increasing antibiotic concentrations. Until complete segregation is achieved, the transformants may be unstable and the integrated sequences can be lost again under nonselective conditions (30, 31).…”

Section: Introductionmentioning

confidence: 99%

Natural transformation of the filamentous cyanobacterium Phormidium lacuna

Nies

Mielke

Pochert

et al. 2019

Preprint

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9Research for biotechnological applications of cyanobacteria focuses on synthetic pathways and 10 bioreactor design, while little effort is devoted to introduce new, promising organisms in the field. 11Applications are most often based on recombinant work, and the establishment of transformation 12 can be a risky, time-consuming procedure. In this work we demonstrate the natural transformation 13 of the filamentous cyanobacterium Phormidium lacuna and insertion of a selection marker into the 14 genome by homologous integration. This is the first example for natural transformation of a member 15 of the order Oscillatoriales. We found that Phormidium lacuna is polyploid, each cell has about 20-16 100 chromosomes. Transformed filaments were resistant against up to 15 mg/ml of kanamycin, and 17 the high resistance feature allowed for rapid segregation into all chromosomes. Formerly, natural 18 transformation in cyanobacteria has been considered a rare and exclusive feature of a few unicellular 19 species. Our finding suggests that natural competence is more distributed among cyanobacteria than 20 previously thought. This is supported by bioinformatic analyses which show that all protein factors 21 for natural transformation are present in the majority of the analyzed cyanobacteria. 22

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Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Cited by 67 publications

References 110 publications

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

Natural transformation of the filamentous cyanobacterium Phormidium lacuna

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