scholarly journals A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes

2011 ◽  
Vol 11 (1) ◽  
pp. 135 ◽  
Author(s):  
Pengcheng Du ◽  
Yinxue Yang ◽  
Haiying Wang ◽  
Di Liu ◽  
George F Gao ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Insertion Sites

scholarly journals Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Courtney M. Thomas ◽  
Najwa Taib ◽  
Simonetta Gribaldo ◽  
Guillaume Borrel
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Genomic Analysis ◽  
Host Adaptation ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Methyl Branch ◽  
Mechanisms Of Adaptation ◽  
Hydrogenotrophic Methanogens ◽  
Almost All

AbstractOther than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.

scholarly journals Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Jianchao Ying ◽  
Jun Ye ◽  
Teng Xu ◽  
Qian Wang ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Rhodococcus Equi ◽  
Comparative Genomic Analysis ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Studies ◽  
Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

scholarly journals Genomic Analysis of Prophages Recovered from Listeria monocytogenes Lysogens Found in Seafood and Seafood-Related Environment

2021 ◽  
Vol 9 (7) ◽  
pp. 1354
Author(s):  
Hue Thi Kim Vu ◽  
Matthew J. Stasiewicz ◽  
Soottawat Benjakul ◽  
Kitiya Vongkamjan
Keyword(s):  
Mitomycin C ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Sequence Comparisons ◽  
Related Sequence ◽  
Geographical Regions ◽  
Insertion Sites ◽  
The Impact

A prophage is a phage-related sequence that is integrated into a bacterial chromosome. Prophages play an important role in bacterial evolution, survival, and persistence. To understand the impact of Listeria prophages on their host genome organizations, this work sequenced two L. monocytogenes strains (134LM and 036LM), previously identified as lysogens by mitomycin C induction. Draft genomes were generated with assembly sizes of 2,953,877 bp and 3,000,399 bp. One intact prophage (39,532 bp) was inserted into the comK gene of the 134LM genome. Two intact prophages (48,684 bp and 39,488 bp) were inserted in tRNA-Lys and elongation-factor genes of the 036LM genome. The findings confirmed the presence of three corresponding induced phages previously obtained by mitomycin C induction. Comparative genomic analysis of three prophages obtained in the newly sequenced lysogens with 61 prophages found in L. monocytogenes genomes, available in public databases, identified six major clusters using whole genome-based phylogenetic analysis. The results of the comparative genomic analysis of the prophage sequences provides knowledge about the diversity of Listeria prophages and their distribution among Listeria genomes in diverse environments, including different sources or geographical regions. In addition, the prophage sequences and their insertion sites contribute to the genomic diversity of L. monocytogenes genomes. These data of prophage sequences, prophage insertion sites, and prophage sequence comparisons, together with ANIb confirmation, could be useful for L. monocytogenes classification by prophages. One potential development could be refinement of prophage typing tools for monitoring or surveillance of L. monocytogenes contamination and transmission.

scholarly journals Comparative Genomic Analysis of the Interferon/Interleukin-10 Receptor Gene Cluster

1999 ◽  
Vol 9 (3) ◽  
pp. 242-250
Author(s):  
Jérôme Reboul ◽  
Katheleen Gardiner ◽  
Danièle Monneron ◽  
Gilles Uzé ◽  
Georges Lutfalla
Keyword(s):  
Gene Cluster ◽  
Large Scale ◽  
Receptor Gene ◽  
Genomic Analysis ◽  
Interleukin 10 ◽  
Comparative Genomic Analysis ◽  
Chromosome 21 ◽  
Comparative Genomic ◽  
Interferon Α ◽  
Link Type

Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to theGART gene. This cluster includes both components of the interferon α/β-receptor (IFNAR1 and IFNAR2) and the second components of the interferon γ-receptor (IFNGR2) and of the IL-10 receptor (IL10R2). We report here the complete gene content of this GART–cytokine receptor gene cluster and the use of comparative genomic analysis to identify chicken IFNAR1, IFNAR2, andIL10R2. We show that the large-scale structure of this locus is conserved in human and chicken but not in the pufferfish Fugu rubripes. This establishes that the receptor components of these host defense mechanisms were fixed in an ancestor of the amniotes. The extraordinary diversification of the interferon ligand family during the evolution of birds and mammals has therefore occured in the context of a fixed receptor structure.[The sequence data described in this paper have been submitted to GenBank under accession nos.AF039904, AF039905, AF039906, AF039907, AF045606, AF082664, AF082665,AF082666, AF082667, and AF083221.]

scholarly journals Comparative analysis of prophage-like elements inHelicobactersp. genomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2012 ◽  
Author(s):  
Xiangyu Fan ◽  
Yumei Li ◽  
Rong He ◽  
Qiang Li ◽  
Wenxing He
Keyword(s):  
Antibiotic Resistance ◽  
Comparative Analysis ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Bacterial Virulence ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Resistance Proteins ◽  
Cluster A ◽  
First Time

Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information onHelicobactersp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. Phylogenetic relationships of Cluster AHelicobacterprophages were investigated. Furthermore, genomes ofHelicobacterprophages from Clusters B, C, and D were analyzed. Interestingly, some putative antibiotic resistance proteins and virulence factors were associated withHelicobacterprophages.

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