Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

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Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance

Journal of Bacteriology ◽

10.1128/jb.00553-19 ◽

2020 ◽

Vol 202 (8) ◽

Author(s):

Minenosuke Matsutani ◽

Nami Matsumoto ◽

Hideki Hirakawa ◽

Yuh Shiwa ◽

Hirofumi Yoshikawa ◽

...

Keyword(s):

Acetic Acid ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Gene Repertoire ◽

Content Type ◽

Acetobacter Pasteurianus ◽

Respiratory Chains

ABSTRACT Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na+/H+ antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na+/H+ antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains. IMPORTANCE Acetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains. The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na+/H+ antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.

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Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer

The Science of The Total Environment ◽

10.1016/j.scitotenv.2017.07.249 ◽

2017 ◽

Vol 609 ◽

pp. 1238-1247 ◽

Cited By ~ 39

Author(s):

Qiang Zhao ◽

Shengjie Yue ◽

Muhammad Bilal ◽

Hongbo Hu ◽

Wei Wang ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic

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Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex

mSystems ◽

10.1128/msystems.00934-20 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Anoop Singh ◽

Mohita Gaur ◽

Vishal Sharma ◽

Palak Khanna ◽

Ankur Bothra ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Common Ancestor ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Last Common Ancestor ◽

Content Type ◽

Type Iii

ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110. The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5′ end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii. This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages. IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.

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Horizontal gene transfer of copper-containing membrane-bound monooxygenase (CuMMO) and di-iron soluble monooxygenase (SDIMO) in ethane- and propane-oxidizing Rhodococcus

Applied and Environmental Microbiology ◽

10.1128/aem.00227-21 ◽

2021 ◽

Author(s):

Bin Zou ◽

Ying Huang ◽

Pan-Pan Zhang ◽

Xiao-Ming Ding ◽

Huub J.M. Op den Camp ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Aerobic Oxidation ◽

Rapid Evolution ◽

Genomic Analysis ◽

Comparative Genomic ◽

Alkane Degradation ◽

Mating Experiment ◽

Soluble Methane Monooxygenase ◽

Membrane Bound

The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are not only involved in methane oxidation but also in short-chain alkane oxidation. Herein, we describe Rhodococcus sp. ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source and report on horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMO) of the CuMMO family and sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear mega-plasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient R. erythropolis in a mating experiment and showed similar ethane and propane consuming activities. Finally, our findings demonstrate that horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. Importance CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient the similar ability to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane-degradation. Our results indicate that plasmids can support rapid evolution of enzyme-mediated biogeochemical processes.

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“Sifarchaeota” a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy

10.1101/2020.10.14.339440 ◽

2020 ◽

Author(s):

Ibrahim F. Farag ◽

Rui Zhao ◽

Jennifer F. Biddle

Keyword(s):

Costa Rica ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Marine Sediments ◽

Genomic Analysis ◽

Comparative Genomic ◽

Deep Sediment ◽

Niche Adaptation ◽

Ecological Roles ◽

Costa Rica Margin

AbstractThe Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic methylotrophy pathway enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. Also, the MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested a similar metabolic potentials and ecological roles. Furthermore, we identified multiple potential horizontal gene transfer (HGT) events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation.ImportanceDeep marine sediments are the home of multiple poorly described archaeal lineages, many of which have ecological and evolutionary importance. We recovered metagenome-assembled genomes (MAGs) belonging to a novel Asgard phylum from the deep sediment of the Costa Rica margin. We proposed the name “Sifarchaeota” to describe the members of this phylum. Representative genomes of the “Sifarchaeota” showed remarkable saccharolytic capacities extending the known metabolic features encoded by the Asgard lineages. We attribute its ability to survive under the deep sediment conditions to its putative capacities to utilize different (C1-C3) compounds commonly encountered in deep sediment environments via anaerobic methylotrophy pathway. Also, we showed the importance of horizontal gene transfer in enhancing the “Sifarchaeota” collective adaptation strategies.

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Comparative genomic analysis reveals an ‘open’ pan‐genome of African swine fever virus

Transboundary and Emerging Diseases ◽

10.1111/tbed.13489 ◽

2020 ◽

Vol 67 (4) ◽

pp. 1553-1562 ◽

Cited By ~ 3

Author(s):

Liang Wang ◽

Yuzi Luo ◽

Yuhui Zhao ◽

George F. Gao ◽

Yuhai Bi ◽

...

Keyword(s):

African Swine Fever Virus ◽

Genomic Analysis ◽

African Swine Fever ◽

Comparative Genomic Analysis ◽

Fever Virus ◽

Comparative Genomic ◽

Pan Genome

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Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T

Marine Drugs ◽

10.3390/md17120661 ◽

2019 ◽

Vol 17 (12) ◽

pp. 661 ◽

Cited By ~ 5

Author(s):

Nadezhda Chernysheva ◽

Evgeniya Bystritskaya ◽

Anna Stenkova ◽

Ilya Golovkin ◽

Olga Nedashkovskaya ◽

...

Keyword(s):

Comparative Genomics ◽

Core Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Active Enzyme ◽

Comparative Genomic ◽

The Core ◽

Pan Genome ◽

Carbohydrate Active Enzyme ◽

Pharmaceutical Industries

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

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Comparative genomic analysis of Mycobacterium tuberculosis reveals evolution and genomic instability within Uganda I sub-lineage

10.1101/2020.10.24.353425 ◽

2020 ◽

Author(s):

Stephen Kanyerezi ◽

Patricia Nabisubi

Keyword(s):

Mycobacterium Tuberculosis ◽

Core Genome ◽

Variant Calling ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Genome Wide Association ◽

Comparative Genomic ◽

Pan Genome ◽

Genome Wide

AbstractIntroductionTuberculosis (TB) is the leading cause of morbidity and mortality globally, responsible for an estimated annual 10.0 million new cases and 1.3 million deaths among infectious diseases with Africa contributing a quarter of these cases in 2019. Classification of Mycobacterium tuberculosis (MTB) strains is important in understanding their geographical predominance and pathogenicity. Different studies have gone ahead to classify MTB using different methods. Some of these include; RFLP, spoligotyping, MIRU-VNTR and SNP set based phylogeny. The SNP set based classification has been found to be in concordance with the region of difference (RD) analysis of MTB complex classification system. In Uganda, the most common cause of pulmonary tuberculosis (PTB) is Uganda genotype of MTB and accounts for up to 70 % of isolates.MethodsSequenced MTB genome samples were retrieved from NCBI and others from local sequencing projects. The genomes were subjected to snippy (a rapid haploid variant calling and core genome alignment) to call variants and annotate them. Outputs from snippy were used to classify the isolates into Uganda genotypes and Non Ugandan genotypes based on 62 SNP set. The Ugandan genotype isolates were later subjected to 413 SNP set and then to a pan genome wide association analysis.Results6 Uganda genotype isolates were found not to classify as either Uganda I or II genotypes based on the 62 SNP set. Using the 413 SNP set, the 6 Uganda genotype isolates were found to have only one SNP out of the 7 SNPs that classify the Uganda I genotypes. They were also found to have both missense and frameshift mutations within the ctpH gene whereas the rest of Uganda I that had a mutation within this gene, was a missense.ConclusionAmong the Uganda genotypes genomes, Uganda I genomes are unstable. We used publicly available datasets to perform analysis like mapping, variant calling, mixed infection, pan-genome analysis to investigate and compare evolution of the Ugandan genotype.

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