scholarly journals Nomadic Lifestyle of Lactobacillus plantarum Revealed by Comparative Genomics of 54 strains Isolated from Different Niches

2016 ◽  
Author(s):  
Maria Elena Martino ◽  
Jumamurat R. Bayjanov ◽  
Brian E. Caffrey ◽  
Michiel Wels ◽  
Pauline Joncour ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Lactobacillus Plantarum ◽  
Functional Divergence ◽  
High Complexity ◽  
Bacterial Genomes ◽  
Genomic Signatures ◽  
Ecological Versatility ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Ecological Constraint

AbstractThe ability of many bacteria to adapt to diverse environmental conditions is well known. Recent research has linked the process of bacterial adaptation to a niche to changes in the genome content and size, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse niches that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of niches. With the aim of unravelling the link between genome evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Phylogenomic analyses coupled with the study of genetic functional divergence and gene-trait matching analysis revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings demonstrate the high complexity of L. plantarum evolution, revealing the absence of specific genomic signatures marking adaptations of this species towards the diverse habitats it is associated with. This suggests fundamentally similar and parallel trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species.

scholarly journals Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Rei Kajitani ◽  
Dai Yoshimura ◽  
Yoshitoshi Ogura ◽  
Yasuhiro Gotoh ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
De Novo ◽  
Bacterial Genomes ◽  
Long Reads ◽  
Wide Range ◽  
Long Read ◽  
Phylogenomic Analyses ◽  
Error Removal ◽  
Iterative Error

Abstract De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

scholarly journals Genome evolution and functional divergence inYersinia

2007 ◽  
Vol 308B (1) ◽  
pp. 37-49 ◽  
Author(s):  
Jianying Gu ◽  
Jennifer L. Neary ◽  
Maribel Sanchez ◽  
Jian Yu ◽  
Timothy G. Lilburn ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Functional Divergence

scholarly journals Cotton genome evolution and features of its structural and functional organization

2020 ◽  
Vol 65 (1) ◽  
Author(s):  
Ksenia Strygina ◽  
Elena Khlestkina ◽  
Larisa Podolnaya
Keyword(s):  
Genome Evolution ◽  
Functional Organization ◽  
Functional Divergence ◽  
Model Organism ◽  
Plant Genome ◽  
Individual Species ◽  
Expression Of Genes ◽  
Genome Duplications ◽  
Allotetraploid Species ◽  
Allotetraploid Cotton

Allotetraploid cotton Gossypium hirsutum L. is not only an important crop, but also a model organism used to study such processes as polyploidization, plant genome evolution and the influence of polyploidy on gene expression. The present article provides a review of studies devoted to the taxonomy of the genus Gossypium, the evolution of the genomes of its representatives (including 45 diploid and 7 allotetraploid species), and the functional divergence of duplicated copies of the same genes in allotetraploid species. The discussion concerns the areas of individual species’ origin, as well as the reasons of the high variation in genome size (from ~880 Mb to ~2400 Mb), which was influenced by both full-genome duplications and the spread of mobile genetic elements. The data support the fact that the expression of genes in allotetraploid cotton changes as a result of polyploidization, and that one of the two subgenomes dominates in the formation of one or another trait. The considered data shed light on the features of the evolution of plant genes and genomes.

scholarly journals A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

2016 ◽  
pp. btw518 ◽  
Author(s):  
Nicole E. Wheeler ◽  
Lars Barquist ◽  
Robert A. Kingsley ◽  
Paul P. Gardner
Keyword(s):  
Functional Divergence ◽  
Bacterial Genomes ◽  
Orthologous Genes

scholarly journals The Lp_3561 and Lp_3562 Enzymes Support a Functional Divergence Process in the Lipase/Esterase Toolkit from Lactobacillus plantarum

2016 ◽  
Vol 7 ◽  
Author(s):  
María Esteban-Torres ◽  
Inés Reverón ◽  
Laura Santamaría ◽  
José M. Mancheño ◽  
Blanca de las Rivas ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Functional Divergence

scholarly journals Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

2020 ◽  
Author(s):  
Itamar Sela ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Genome Size ◽  
Bacterial Genomes ◽  
Prokaryotic Genomes ◽  
Simplifying Assumptions ◽  
Specific Shape ◽  
Foreign Genes ◽  
The Cost

AbstractThe genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. To elucidate the evolutionary factors that define the specific shape of this distribution, we investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genomes intersections for 33 groups of closely related bacterial genomes. The combined analysis of genome intersections and gene commonality shows that at least one of the two simplifying assumptions that are usually adopted for modeling the evolution of the U-shaped distribution, those of infinitely many genes and constant genome size, is invalid. The violation of both these assumptions stems from the horizontal gene transfer barrier, i.e. the cost of accommodation of foreign genes by prokaryotes.

scholarly journals Genome size evolution in the Archaea

2018 ◽  
Vol 2 (4) ◽  
pp. 595-605 ◽  
Author(s):  
Siri Kellner ◽  
Anja Spang ◽  
Pierre Offre ◽  
Gergely J. Szöllősi ◽  
Celine Petitjean ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Size ◽  
Prokaryotic Genome ◽  
Ecological Niches ◽  
Cellular Life ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Genome Level ◽  
Phylogenomic Analyses

What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.

scholarly journals Genomic GC content drifts slowly downward in most bacterial genomes

2020 ◽  
Author(s):  
Bert Ely
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Base Pairs ◽  
Wide Range ◽  
Biased Gene Conversion ◽  
Prokaryotic Genomes ◽  
Genome Content ◽  
Genomic Gc Content ◽  
Eukaryotic Genomes

AbstractIn every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is slowly declining in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing at a slow rate. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genome content as well.

scholarly journals Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

2021 ◽  
Vol 12 ◽  
Author(s):  
Yisong Li ◽  
Meng Wang ◽  
Zhong-Zhi Sun ◽  
Bin-Bin Xie
Keyword(s):  
Secondary Metabolism ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Genomic Features ◽  
Separate Genus ◽  
The Family ◽  
Genomic Analyses ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Close Relatives

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

scholarly journals Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

2020 ◽  
Vol 8 (11) ◽  
pp. 1713
Author(s):  
Zhi Yong Shen ◽  
Xiu Pei Koh ◽  
Yan Ping Yu ◽  
Stanley C. K. Lau
Keyword(s):  
Functional Divergence ◽  
Low Frequency ◽  
Independent Set ◽  
Correct Prediction ◽  
Habitat Association ◽  
Orthologous Genes ◽  
Genomic Signatures ◽  
Environment Model ◽  
Niche Adaptation ◽  
External Environments

The evolution, habitat, and lifestyle of the cryptic clade II of Escherichia, which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other Escherichia genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments.

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