scholarly journals Comparative analysis of prophages in Streptococcus mutans genomes

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4057 ◽  
Author(s):  
Tiwei Fu ◽  
Xiangyu Fan ◽  
Quanxin Long ◽  
Wanyan Deng ◽  
Jinlin Song ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Major Gene ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Phenotypic Properties ◽  
Integrase Gene ◽  
Protein Modules

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages.

scholarly journals Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

2009 ◽  
Vol 191 (15) ◽  
pp. 4854-4862 ◽  
Author(s):  
Patricia Romero ◽  
Nicholas J. Croucher ◽  
N. Luisa Hiller ◽  
Fen Z. Hu ◽  
Garth D. Ehrlich ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Major Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Bioinformatic Tools ◽  
Dichelobacter Nodosus ◽  
First Time

ABSTRACT Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage φSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Biology and Genome Sequence of Streptococcus mutans Phage M102AD

2012 ◽  
Vol 78 (7) ◽  
pp. 2264-2271 ◽  
Author(s):  
Allan L. Delisle ◽  
Ming Guo ◽  
Natalia I. Chalmers ◽  
Gerard J. Barcak ◽  
Geneviève M. Rousseau ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Streptococcus Thermophilus ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Content Type ◽  
Close Relationship ◽  
Virion Structure

ABSTRACTM102AD is the new designation for aStreptococcus mutansphage described in 1993 as phage M102. This change was necessitated by the genome analysis of anotherS. mutansphage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed thatS. mutansphage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains ofS. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3′-overhangcossite that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship betweenS. mutansphages M102AD and M102 as well as withStreptococcus thermophilusphages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Genomic Diversity ofLactobacillus salivarius

2010 ◽  
Vol 77 (3) ◽  
pp. 954-965 ◽  
Author(s):  
Emma J. Raftis ◽  
Elisa Salvetti ◽  
Sandra Torriani ◽  
Giovanna E. Felis ◽  
Paul W. O'Toole
Keyword(s):  
Hot Spots ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Phenotypic Traits ◽  
Lactobacillus Salivarius ◽  
Genome Content ◽  
High Level ◽  
Selection Of

ABSTRACTStrains ofLactobacillus salivariusare increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity ofL. salivariushas been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals.L. salivariusdisplays a high level of genomic diversity, and while selection ofL. salivariusstrains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.

scholarly journals Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 754
Author(s):  
Yupeng Wu ◽  
Hui Fang ◽  
Jiping Wen ◽  
Juping Wang ◽  
Tianwen Cao ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Cox1 Gene ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

scholarly journals Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

scholarly journals Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae

2020 ◽  
Author(s):  
Andy O. Leu ◽  
Simon J. McIlroy ◽  
Jun Ye ◽  
Donovan H. Parks ◽  
Victoria J. Orphan ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Anaerobic Oxidation Of Methane ◽  
Metabolic Potential ◽  
Oxidation Of Methane ◽  
Oxidation Of Hydrogen ◽  
Global Biogeochemical Cycles

AbstractAnaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners.ImportanceAOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance to the global carbon cycle and climate change modelling. While the oxidation of methane coupled to sulphate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae as they are absent in related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.

scholarly journals Interspecies Genomic Variation and Transcriptional Activeness of Secondary Metabolism-Related Genes in Aspergillus Section Fumigati

2021 ◽  
Vol 2 ◽  
Author(s):  
Hiroki Takahashi ◽  
Maiko Umemura ◽  
Akihiro Ninomiya ◽  
Yoko Kusuya ◽  
Masaaki Shimizu ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Closely Related Species ◽  
Unknown Reason ◽  
Neosartorya Fischeri ◽  
Fungal Secondary Metabolism ◽  
Respective Species

Filamentous fungi produce various bioactive compounds that are biosynthesized by sets of proteins encoded in biosynthesis gene clusters (BGCs). For an unknown reason, many BGCs are transcriptionally silent in laboratory conditions, which has hampered the discovery of novel fungal compounds. The transcriptional reactiveness of fungal secondary metabolism is not fully understood. To gain the comprehensive view, we conducted comparative genomic and transcriptomic analyses of nine closely-related species of Aspergillus section Fumigati (A. fumigatus, A. fumigatiaffinis, A. novofumigatus, A. thermomutatus, A. viridinutans, A. pseudoviridinutans, A. lentulus, A. udagawae, and Neosartorya fischeri). For expanding our knowledge, we newly sequenced genomes of A. viridinutans and A. pseudoviridinutans, and reassembled and reannotated the previously released genomes of A. lentulus and A. udagawae. Between 34 and 84 secondary metabolite (SM) backbone genes were identified in the genomes of these nine respective species, with 8.7–51.2% being unique to the species. A total of 247 SM backbone gene types were identified in the nine fungi. Ten BGCs are shared by all nine species. Transcriptomic analysis using A. fumigatus, A. lentulus, A. udagawae, A. viridinutans, and N. fischeri was conducted to compare expression levels of all SM backbone genes in four different culture conditions; 32–83% of SM backbone genes in these species were not expressed in the tested conditions, which reconfirmed that large part of fungal SM genes are hard to be expressed. The species-unique SM genes of the five species were expressed with lower frequency (18.8% in total) than the SM genes that are conserved in all five species (56%). These results suggest that the expression tendency of BGCs is correlated with their interspecies distribution pattern. Our findings increase understanding of the evolutionary processes associated with the regulation of fungal secondary metabolism.

scholarly journals Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

Abstract Background: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.

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