scholarly journals The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family

2014 ◽  
Vol 89 (6) ◽  
pp. 3008-3025 ◽  
Author(s):  
Annie Bézier ◽  
Julien Thézé ◽  
Frederick Gavory ◽  
Julien Gaillard ◽  
Julie Poulain ◽  
...  
Keyword(s):  
New Genus ◽  
Brown Planthopper ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Body Protein ◽  
Content Type ◽  
Occlusion Bodies ◽  
Phylogenomic Analyses ◽  
Dsdna Viruses ◽  
Core Genes

ABSTRACTA large double-stranded DNA (dsDNA) virus that produces occlusion bodies, typical of baculoviruses, has been described to infect crane fly larvae of the genusTipula(Diptera, Tipulidae). Because of a lack of genomic data, this virus has remained unclassified. Electron microscopy of an archival virus isolated fromTipula oleracea,T. oleraceanudivirus (ToNV), showed irregularly shaped occlusion bodies measuring from 2 to 5 μm in length and 2 μm in middiameter, filled with rod-shape virions containing single nucleocapsids within a bilayer envelope. Whole-genome amplification and Roche 454 sequencing revealed a complete circular genome sequence of 145.7 kb, containing five direct repeat regions. We predicted 131 open reading frames, including a homolog of the polyhedrin gene encoding the major occlusion body protein ofT. paludosanucleopolyhedrovirus (NPV). BLAST searches demonstrated that ToNV had 21 of the 37 baculovirus core genes but shared 52 genes with nudiviruses (NVs). Phylogenomic analyses indicated that ToNV clearly belongs to theNudiviridaefamily but should probably be assigned to a new genus. Among nudiviruses, ToNV was most closely related to thePenaeus monodonNV andHeliothis zeaNV clade but distantly related toDrosophila innubiaNV, the other nudivirus infecting a Diptera. Lastly, ToNV was found to be most closely related to the nuvidirus ancestor of bracoviruses. This was also reflected in terms of gene content, as ToNV was the only known exogenous virus harboring homologs of theCc50C22.6and27b(Cc50C22.7) genes found in the nudiviral genomic cluster involved in bracovirus particle production.IMPORTANCETheNudiviridaeis a family of arthropod dsDNA viruses from which striking cases of endogenization have been reported (i.e., symbiotic bracoviruses deriving from a nudivirus and the endogenous nudivirus of the brown planthopper). Although related to baculoviruses, relatively little is known about the genomic diversity of exogenous nudiviruses. Here, we characterized, morphologically and genetically, an archival sample of theTipula oleraceanudivirus (ToNV), which has the particularity of forming occlusion bodies. Comparative genomic and phylogenomic analyses showed ToNV to be to date the closest known relative of the exogenous ancestor of bracoviruses and that ToNV should be assigned to a new genus. Moreover, we revised the homology relationships of nudiviral genes and identified a new set of 32 core genes for theNudiviridae, of which 21 were also baculovirus core genes. These findings provide important insights into the evolutionary history of large arthropod dsDNA viruses.

scholarly journals Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

2014 ◽  
Vol 80 (15) ◽  
pp. 4616-4625 ◽  
Author(s):  
Thomas Denes ◽  
Kitiya Vongkamjan ◽  
Hans-Wolfgang Ackermann ◽  
Andrea I. Moreno Switt ◽  
Martin Wiedmann ◽  
...  
Keyword(s):  
New York ◽  
Dairy Farm ◽  
Morphological Diversity ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
The Novel ◽  
Important Food ◽  
Content Type ◽  
Small Genome ◽  
Food Borne

ABSTRACTThe genusListeriais ubiquitous in the environment and includes the globally important food-borne pathogenListeria monocytogenes. While the genomic diversity ofListeriahas been well studied, considerably less is known about the genomic and morphological diversity ofListeriabacteriophages. In this study, we sequenced and analyzed the genomes of 14Listeriaphages isolated mostly from New York dairy farm environments as well as one relatedEnterococcus faecalisphage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. TheseListeriaphages, based on gene orthology and morphology, together with previously sequencedListeriaphages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) ofE. faecalisphages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novelListeriaphage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

scholarly journals Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes

2013 ◽  
Vol 13 (1) ◽  
pp. 143-153 ◽  
Author(s):  
Anastasios D. Tsaousis ◽  
Eleni Gentekaki ◽  
Laura Eme ◽  
Daniel Gaston ◽  
Andrew J. Roger
Keyword(s):  
Subcellular Fractionation ◽  
Comparative Genomic ◽  
Cluster Assembly ◽  
Iron Sulfur Cluster ◽  
Content Type ◽  
Sulfur Cluster ◽  
Evolutionary Diversification ◽  
Iron Sulfur ◽  
History Of ◽  
Phylogenomic Analyses

ABSTRACT The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight proteins in opisthokont lineages, such as animals and fungi. We sought to identify and characterize homologues of the CIA system proteins in the anaerobic stramenopile parasite Blastocystis sp. strain NandII. We identified transcripts encoding six of the components—Cia1, Cia2, MMS19, Nbp35, Nar1, and a putative Tah18—and showed using immunofluorescence microscopy, immunoelectron microscopy, and subcellular fractionation that the last three of them localized to the cytoplasm of the cell. We then used comparative genomic and phylogenetic approaches to investigate the evolutionary history of these proteins. While most Blastocystis homologues branch with their eukaryotic counterparts, the putative Blastocystis Tah18 seems to have a separate evolutionary origin and therefore possibly a different function. Furthermore, our phylogenomic analyses revealed that all eight CIA components described in opisthokonts originated before the diversification of extant eukaryotic lineages and were likely already present in the last eukaryotic common ancestor (LECA). The Nbp35, Nar1 Cia1, and Cia2 proteins have been conserved during the subsequent evolutionary diversification of eukaryotes and are present in virtually all extant lineages, whereas the other CIA proteins have patchy phylogenetic distributions. Cia2 appears to be homologous to SufT, a component of the prokaryotic sulfur utilization factors (SUF) system, making this the first reported evolutionary link between the CIA and any other Fe/S biogenesis pathway. All of our results suggest that the CIA machinery is an ubiquitous biosynthetic pathway in eukaryotes, but its apparent plasticity in composition raises questions regarding how it functions in nonmodel organisms and how it interfaces with various iron/sulfur cluster systems (i.e., the iron/sulfur cluster, nitrogen fixation, and/or SUF system) found in eukaryotic cells.

scholarly journals Leptospire Genomic Diversity Revealed by Microarray-Based Comparative Genomic Hybridization

2012 ◽  
Vol 78 (9) ◽  
pp. 3045-3050 ◽  
Author(s):  
Broderick Eribo ◽  
Sirima Mingmongkolchai ◽  
Tingfen Yan ◽  
Padunsri Dubbs ◽  
Karen E. Nelson
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Virulence Factors ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Leptospira Interrogans ◽  
Genomic Hybridization ◽  
Content Type ◽  
Reference Genomes

ABSTRACTComparative genomic hybridization was used to compare genetic diversity of five strains ofLeptospira(Leptospira interrogansserovars Bratislava, Canicola, and Hebdomadis andLeptospira kirschneriserovars Cynopteri and Grippotyphosa). The array was designed based on two available sequencedLeptospirareference genomes, those ofL. interrogansserovar Copenhageni andL. interrogansserovar Lai. A comparison of genetic contents showed thatL. interrogansserovar Bratislava was closest to the reference genomes whileL. kirschneriserovar Grippotyphosa had the least similarity to the reference genomes. Cluster analysis indicated thatL. interrogansserovars Bratislava and Hebdomadis clustered together first, followed byL. interrogansserovar Canicola, before the twoL. kirschneristrains. Confirmed/potential virulence factors identified in previous research were also detected in the tested strains.

scholarly journals Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Chiara Tarracchini ◽  
Gabriele Andrea Lugli ◽  
Leonardo Mancabelli ◽  
Christian Milani ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Human Population ◽  
Gardnerella Vaginalis ◽  
Comparative Genomic ◽  
Genetic Traits ◽  
Content Type ◽  
Microbial Taxon ◽  
Virulence Potential ◽  
Genomic Analyses ◽  
Phylogenomic Analyses

ABSTRACT Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance. IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.

scholarly journals Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon

2021 ◽  
Vol 7 (7) ◽  
Author(s):  
Chiara Tarracchini ◽  
Christian Milani ◽  
Gabriele Andrea Lugli ◽  
Leonardo Mancabelli ◽  
Federico Fontana ◽  
...  
Keyword(s):  
Type Species ◽  
Mammalian Species ◽  
Bifidobacterium Longum ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Content Type ◽  
Link Type ◽  
Physiological Diversity ◽  
Genetic Features

Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum , B. longum subsp. infantis and B. longum subsp. suis . Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.

scholarly journals Exploration of the Genomic Diversity and Core Genome of the Bifidobacterium adolescentis Phylogenetic Group by Means of a Polyphasic Approach

2012 ◽  
Vol 79 (1) ◽  
pp. 336-346 ◽  
Author(s):  
Sabrina Duranti ◽  
Francesca Turroni ◽  
Christian Milani ◽  
Elena Foroni ◽  
Francesca Bottacini ◽  
...  
Keyword(s):  
Core Genome ◽  
Phylogenetic Group ◽  
Genomic Diversity ◽  
Polyphasic Approach ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Genome Diversity ◽  
Genome Sequences ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e., Bifidobacterium adolescentis , Bifidobacterium catenulatum , and Bifidobacterium pseudocatenulatum , by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.

scholarly journals A taxogenomics approach uncovers a new genus in the phylum Placozoa

2017 ◽  
Author(s):  
Michael Eitel ◽  
Warren R. Francis ◽  
Hans-Jürgen Osigus ◽  
Stefan Krebs ◽  
Sergio Vargas ◽  
...  
Keyword(s):  
New Genus ◽  
Single Gene ◽  
Nuclear Genome ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Marine Animals ◽  
Additional Species ◽  
Worldwide Distribution ◽  
Phylogenomic Analyses ◽  
Taxonomic Framework

AbstractThe Placozoa [1] is a monotypic phylum of non-bilaterian marine animals. Its only species, Trichoplax adhaerens, was described in 1883 [2], Despite the worldwide distribution of placozoans [3–6], morphological differences are lacking among isolates from different geographic areas and, consequently, no other species in this phylum has been described and accepted for more than 130 years. However, recent single-gene studies on the genetic diversity of this “species” have revealed deeply divergent lineages of, as yet, undefined taxonomic ranks [3,5,6], Since single genes are not considered sufficient to define species [7], a whole nuclear genome comparison appears the most appropriate approach to determine relationships between placozoan lineages. Such a “taxogenomics” approach can help discover and diagnose potential additional species and, therefore, develop a much-needed, more robust, taxonomic framework for this phylum. To achieve this we sequenced the genome of a placozoan lineage isolated from Hong Kong (lineage H13), which is distantly related to T. adhaerens [6]. The 87 megabase genome assembly contains 12,010 genes. Comparison to the T. adhaerens genome [8] identified an average protein distance of 24.4% in more than 2,700 screened one-to-one orthologs, similar to levels observed between the chordate classes mammals and birds. Genome rearrangements are commonplace and >25% of genes are not collinear (i.e. they are not in the same order in the two genomes). Finally, a multi-gene distance comparison with other non-bilaterian phyla indicate genus level differences to T. adhaerens. These data highlight the large genomic diversity within the Placozoa and justifies the designation of lineage HI3 as a new species, Xxxxxxxxx yyyyyyyyyyyyy1 gen. et spaec. nov., now the second described placozoan species and the first in a new genus. Phylogenomic analyses furthermore supports a robust placement of the Placozoa as sister to a cnidarian-bilaterian clade.

scholarly journals Role of Homologous Recombination in Adaptive Diversification of Extraintestinal Escherichia coli

2012 ◽  
Vol 195 (2) ◽  
pp. 231-242 ◽  
Author(s):  
Sandip Paul ◽  
Elena V. Linardopoulou ◽  
Mariya Billig ◽  
Veronika Tchesnokova ◽  
Lance B. Price ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Bacterial Pathogens ◽  
Genomic Diversity ◽  
Fluoroquinolone Resistance ◽  
Content Type ◽  
Adaptive Diversification ◽  
E Coli ◽  
And Function ◽  
Core Genes

ABSTRACTThe contribution of homologous exchange (recombination) of core genes in the adaptive evolution of bacterial pathogens is not well understood. To investigate this, we analyzed fully assembled genomes of twoEscherichia colistrains from sequence type 131 (ST131), a clonal group that is both the leading cause of extraintestinalE. coliinfections and the main source of fluoroquinolone-resistantE. coli. Although the sequences of each of the seven multilocus sequence typing genes were identical in the two ST131 isolates, the strains diverged from one another by homologous recombination that affected at least 9% of core genes. This was on a par with the contribution to genomic diversity of horizontal gene transfer and point gene mutation. The genomic positions of recombinant and mobile genetic regions were partially linked, suggesting their concurrent occurrence. One of the genes affected by homologous recombination wasfimH, which encodes mannose-specific type 1 fimbrial adhesin, resulting in functionally distinct copies of the gene in ST131 strains. One strain, a uropathogenic isolate, had a pathoadaptive variant offimHthat was acquired by homologous replacement into the commensal strain background. Close examination of FimH structure and function in additional ST131 isolates revealed that recombination led to acquisition of several functionally distinct variants that, upon homologous exchange, were targeted by a variety of pathoadaptive mutations under strong positive selection. Different recombinantfimHstrains also showed a strong clonal association with ST131 isolates that had distinct fluoroquinolone resistance profiles. Thus, homologous recombination of core genes plays a significant role in adaptive diversification of bacterial pathogens, especially at the level of clonally related groups of isolates.

scholarly journals Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs

mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Katherine E. Bowden ◽  
Sandeep J. Joseph ◽  
John C. Cartee ◽  
Noa Ziklo ◽  
Damien Danavall ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Intracellular Bacterium ◽  
Genomic Diversity ◽  
Clinical Samples ◽  
Comparative Genomic ◽  
Sexual Networks ◽  
Whole Genome ◽  
Target Enrichment ◽  
Content Type ◽  
Sex With Men

ABSTRACT Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelectXT target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men. IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.

scholarly journals Interaction of the Aspergillus nidulans Microtubule-Organizing Center (MTOC) Component ApsB with Gamma-Tubulin and Evidence for a Role of a Subclass of Peroxisomes in the Formation of Septal MTOCs

2010 ◽  
Vol 9 (5) ◽  
pp. 795-805 ◽  
Author(s):  
Nadine Zekert ◽  
Daniel Veith ◽  
Reinhard Fischer
Keyword(s):  
Aspergillus Nidulans ◽  
Protein Complexes ◽  
Spindle Pole ◽  
Eukaryotic Cells ◽  
Microtubule Organizing Center ◽  
Body Protein ◽  
Content Type ◽  
C Terminus ◽  
Peroxisomal Targeting ◽  
Gamma Tubulin

ABSTRACT Peroxisomes are a diverse class of organelles involved in different physiological processes in eukaryotic cells. Although proteins imported into peroxisomes carry a peroxisomal targeting sequence at the C terminus (PTS1) or an alternative one close to the N terminus (PTS2), the protein content of peroxisomes varies drastically. Here we suggest a new class of peroxisomes involved in microtubule (MT) formation. Eukaryotic cells assemble MTs from distinct points in the cell. In the fungus Aspergillus nidulans, septum-associated microtubule-organizing centers (sMTOCs) are very active in addition to the spindle pole bodies (SPBs). Previously, we identified a novel MTOC-associated protein, ApsB (Schizosaccharomyces pombe mto1), whose absence affected MT formation from sMTOCs more than from SPBs, suggesting that the two protein complexes are organized differently. We show here that sMTOCs share at least two further components, gamma-tubulin and GcpC (S. pombe Alp6) with SPBs and found that ApsB interacts with gamma-tubulin. In addition, we discovered that ApsB interacts with the Woronin body protein HexA and is targeted to a subclass of peroxisomes via a PTS2 peroxisomal targeting sequence. The PTS2 motif was necessary for function but could be replaced with a PTS1 motif at the C terminus of ApsB. These results suggest a novel function for a subclass of peroxisomes in cytoskeletal organization.

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