scholarly journals Towards a better understanding of the bacterial pan-genome

2021 ◽  
Vol 17 ◽  
pp. 84-96
Author(s):  
Dawid Gmiter ◽  
Sylwia Nawrot ◽  
Ilona Pacak ◽  
Katarzyna Zegadło ◽  
Wiesław Kaca
Keyword(s):  
Population Structure ◽  
Bacterial Genome ◽  
Species Level ◽  
Genome Sequences ◽  
Pan Genome ◽  
Multiple Genes ◽  
Number Of Genes ◽  
Structure Diversity

The bacterial pan-genome is a relatively new concept that refers to the number of genes observed in a given set of bacterial genome sequences, either at the intra- or inter-species level. Determining the pan-genome of a given species of bacteria using a large number of strains allows one to compare multiple genes and to determine evolutionary links between isolates. This information can help to determine population structure, diversity in terms of prevalence in a given environment and pathogenicity of microorganisms. Within this review, we explain the most important issues related to pan-genome studies. We also include a brief description of some selected bacterial pan-genomes. Finally, we propose an easy-toperform workflow to study bacterial pan-genomes that will facilitate nonexperts in a pan-genome-based investigation.

scholarly journals Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos (Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin

2021 ◽  
Vol 7 (1) ◽  
pp. 54
Author(s):  
Eduardo Bagagli ◽  
Daniel Ricardo Matute ◽  
Hans Garcia Garces ◽  
Bernardo Guerra Tenório ◽  
Adalberto Garcia Garces ◽  
...  
Keyword(s):  
Population Structure ◽  
Latin America ◽  
Endemic Area ◽  
Amazon Basin ◽  
Paracoccidioides Brasiliensis ◽  
Pathogenic Fungi ◽  
Sensu Stricto ◽  
Species Level ◽  
Dasypus Novemcinctus ◽  
Show Evidence

Paracoccidioidomycosis is an endemic fungal disease to Latin America caused by at least five species-level genotypes of Paracoccidioides, named P. lutzii, P. brasiliensis (S1a and S1b populations), P. americana, P. restrepiensis, and P. venezuelensis. In this manuscript, we report on Paracoccidioides sp. sampling efforts in armadillos from two different areas in Brazil. We sequenced the genomes of seven Paracoccidioides isolates and used phylogenomics and populations genetics for genotyping. We found that P. brasiliensis and P. lutzii are both present in the Amazon region. Additionally, we identified two Paracoccidioides isolates that seem to be the result of admixture between divergent populations within P. brasiliensis sensu stricto. Both of these isolates were recovered from armadillos in a P. lutzii endemic area in Midwestern Brazil. Additionally, two isolates from human patients also show evidence of resulting from admixture. Our results suggest that the populations of P. brasiliensis sensu stricto exchange genes in nature. More generally, they suggest that population structure and admixture within species is an important source of variation for pathogenic fungi.

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

2020 ◽  
Author(s):  
Idowu Olawoye ◽  
Simon D.W. Frost ◽  
Christian T. Happi
Keyword(s):  
West Africa ◽  
Genome Analysis ◽  
West African ◽  
Multiple Copy ◽  
Genome Sequences ◽  
Animal Reservoir ◽  
Pan Genome ◽  
Lineage Specificity ◽  
Mycobacterium Africanum ◽  
Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

scholarly journals Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Sean P. Gordon ◽  
Bruno Contreras-Moreira ◽  
Daniel P. Woods ◽  
David L. Des Marais ◽  
Diane Burgess ◽  
...  
Keyword(s):  
Population Structure ◽  
Brachypodium Distachyon ◽  
Gene Content ◽  
Pan Genome ◽  
Content Variation

scholarly journals Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

2006 ◽  
Vol 70 (2) ◽  
pp. 472-509 ◽  
Author(s):  
Mark K. Ashby ◽  
Jean Houmard
Keyword(s):  
Regulatory Mechanisms ◽  
Genome Plasticity ◽  
Cyanobacterial Genome ◽  
Response Regulators ◽  
Genome Sequences ◽  
Histidine Kinases ◽  
Physiological Properties ◽  
Two Component ◽  
Different Strains ◽  
Structure Diversity

SUMMARY A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.

Detecting density dependence from spatial patterns in a heterogeneous subtropical forest of central China

2015 ◽  
Vol 45 (6) ◽  
pp. 710-720 ◽  
Author(s):  
Yili Guo ◽  
Zhijun Lu ◽  
Qinggang Wang ◽  
Junmeng Lu ◽  
Yaozhan Xu ◽  
...  
Keyword(s):  
Population Structure ◽  
Density Dependence ◽  
Habitat Heterogeneity ◽  
Species Traits ◽  
Subtropical Forest ◽  
Species Level ◽  
Central China ◽  
Life Stages ◽  
Natural Forests ◽  
Level Variation

Accumulating evidence suggests that density dependence, whether at early or late life stages, is an important mechanism regulating plant population structure. However, the opposing effects of habitat heterogeneity and species-level variation might have confounded the prevalence of density dependence in natural forests. These compatible ideas were rarely considered simultaneously. In this study, we applied a spatial statistical technique to examine (i) the prevalence of density dependence at late life stages after controlling for habitat heterogeneity and (ii) the relationships between species traits and the strength of density dependence in a newly established, 25 ha subtropical mountain forest plot in central China. Of the 88 (75%) tree species analyzed, 66 were found to exhibit density dependence predominantly at very close distances among neighbors in the species-rich subtropical forest. In addition, the strength of density dependence was associated with species traits. Our findings identified strong density dependence among trees that had greater stature and were rarer. We concluded that density dependence was a prevalent mechanism for regulating the population structure of most tree species and both habitat heterogeneity and species-level variation played crucial roles in shaping the strength of density dependence in natural forests.

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