Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum , they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.

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Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

Microorganisms ◽

10.3390/microorganisms8122043 ◽

2020 ◽

Vol 8 (12) ◽

pp. 2043

Author(s):

Shawn M. Higdon ◽

Bihua C. Huang ◽

Alan B. Bennett ◽

Bart C. Weimer

Keyword(s):

Machine Learning ◽

Nitrogen Fixation ◽

Genome Wide Association Study ◽

Population Genomics ◽

Genomic Analysis ◽

Oxidation Reduction ◽

Genome Wide ◽

Biological Nitrogen ◽

Carbohydrate Catabolism ◽

Comparative Population

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

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Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

10.1101/536854 ◽

2019 ◽

Author(s):

Devani Romero Picazo ◽

Tal Dagan ◽

Rebecca Ansorge ◽

Jillian M. Petersen ◽

Nicole Dubilier ◽

...

Keyword(s):

Bacterial Colonization ◽

Gill Tissue ◽

Genetic Isolation ◽

Isolated Populations ◽

Genome Wide ◽

Colonization Dynamics ◽

Symbiont Transmission ◽

Environmental Bacteria ◽

Host Life ◽

High Degree

AbstractEukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated populations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life-cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

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Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony

10.21203/rs.3.rs-21864/v1 ◽

2020 ◽

Author(s):

Hojjat Asadollahpour Nanaei ◽

Ali Esmailizadeh ◽

Ahmad Ayatollahi Mehrgardi ◽

Han Jianlin ◽

Dong-Dong Wu ◽

...

Keyword(s):

Body Size ◽

Positive Selection ◽

Nucleotide Diversity ◽

Population Genomics ◽

Small Body ◽

Composite Likelihood ◽

The Body ◽

Fixation Index ◽

Small Body Size ◽

Comparative Population

Abstract Background Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi), and further analyzed the results to find genomic regions under selection for body size-related traits.Results A number of protein-coding genes with significant (P-value < 0.01) higher FST values (367 genes), XP-CLR scores (681 genes), and a lower value for nucleotide diversity (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have independently been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size.Conclusions Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.

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