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 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 TOUCAN: a framework for fungal biosynthetic gene cluster discovery

2020 ◽  
Vol 2 (4) ◽  
Author(s):  
Hayda Almeida ◽  
Sylvester Palys ◽  
Adrian Tsang ◽  
Abdoulaye Baniré Diallo
Keyword(s):  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Amino Acid Sequences ◽  
Genomic Diversity ◽  
Complex Task ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Learning Framework ◽  
Limited Scope ◽  
Selection Of

Abstract Fungal secondary metabolites (SMs) are an important source of numerous bioactive compounds largely applied in the pharmaceutical industry, as in the production of antibiotics and anticancer medications. The discovery of novel fungal SMs can potentially benefit human health. Identifying biosynthetic gene clusters (BGCs) involved in the biosynthesis of SMs can be a costly and complex task, especially due to the genomic diversity of fungal BGCs. Previous studies on fungal BGC discovery present limited scope and can restrict the discovery of new BGCs. In this work, we introduce TOUCAN, a supervised learning framework for fungal BGC discovery. Unlike previous methods, TOUCAN is capable of predicting BGCs on amino acid sequences, facilitating its use on newly sequenced and not yet curated data. It relies on three main pillars: rigorous selection of datasets by BGC experts; combination of functional, evolutionary and compositional features coupled with outperforming classifiers; and robust post-processing methods. TOUCAN best-performing model yields 0.982 F-measure on BGC regions in the Aspergillus niger genome. Overall results show that TOUCAN outperforms previous approaches. TOUCAN focuses on fungal BGCs but can be easily adapted to expand its scope to process other species or include new features.

scholarly journals Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis

2009 ◽  
Vol 191 (14) ◽  
pp. 4492-4501 ◽  
Author(s):  
Keh-Ming Wu ◽  
Ling-Hui Li ◽  
Jing-Jou Yan ◽  
Nina Tsao ◽  
Tsai-Lien Liao ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Liver Abscess ◽  
Nosocomial Infections ◽  
Capsular Polysaccharide ◽  
Gene Clusters ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Major Health Problem

ABSTRACT Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a major health problem worldwide, while community-acquired K. pneumoniae infections present with a range of diverse clinical pictures in different geographic areas. In particular, an invasive form of K. pneumoniae that causes liver abscesses was first observed in Asia and then was found worldwide. We are interested in how differences in gene content of the same species result in different diseases. Thus, we sequenced the whole genome of K. pneumoniae NTUH-K2044, which was isolated from a patient with liver abscess and meningitis, and analyzed differences compared to strain MGH 78578, which was isolated from a patient with pneumonia. Six major types of differences were found in gene clusters that included an integrative and conjugative element, clusters involved in citrate fermentation, lipopolysaccharide synthesis, and capsular polysaccharide synthesis, phage-related insertions, and a cluster containing fimbria-related genes. We also conducted comparative genomic hybridization with 15 K. pneumoniae isolates obtained from community-acquired or nosocomial infections using tiling probes for the NTUH-K2044 genome. Hierarchical clustering revealed three major groups of genomic insertion-deletion patterns that correlate with the strains' clinical features, antimicrobial susceptibilities, and virulence phenotypes with mice. Here we report the whole-genome sequence of K. pneumoniae NTUH-K2044 and describe evidence showing significant genomic diversity and sequence acquisition among K. pneumoniae pathogenic strains. Our findings support the hypothesis that these factors are responsible for the changes that have occurred in the disease profile over time.

scholarly journals Genome-Wide Analysis of Ruminant Staphylococcus aureus Reveals Diversification of the Core Genome

2008 ◽  
Vol 190 (19) ◽  
pp. 6302-6317 ◽  
Author(s):  
Nouri L. Ben Zakour ◽  
Daniel E. Sturdevant ◽  
Sergine Even ◽  
Caitriona M. Guinane ◽  
Corinne Barbey ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Core Genome ◽  
Allelic Variation ◽  
Genomic Variation ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Extensive Variation ◽  
Genes Encoding ◽  
Genome Content

ABSTRACT Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus, we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of S. aureus host adaptation.

scholarly journals Genetic Diversity of Toxigenic and Nontoxigenic Vibrio cholerae Serogroups O1 and O139 Revealed by Array-Based Comparative Genomic Hybridization

2007 ◽  
Vol 189 (13) ◽  
pp. 4837-4849 ◽  
Author(s):  
Bo Pang ◽  
Meiying Yan ◽  
Zhigang Cui ◽  
Xiaofen Ye ◽  
Baowei Diao ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Clonal Selection ◽  
Gene Clusters ◽  
Small Chromosome ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Pathogenic Potential ◽  
Genomic Microarray ◽  
Ctx Prophage ◽  
El Tor

ABSTRACT Toxigenic serogroups O1 and O139 of Vibrio cholerae may cause cholera epidemics or pandemics. Nontoxigenic strains within these serogroups also exist in the environment, and also some may cause sporadic cases of disease. Herein, we investigate the genomic diversity among toxigenic and nontoxigenic O1 and O139 strains by comparative genomic microarray hybridization with the genome of El Tor strain N16961 as a base. Conservation of the toxigenic O1 El Tor and O139 strains is found as previously reported, whereas accumulation of genome changes was documented in toxigenic El Tor strains isolated within the 40 years of the seventh pandemic. High phylogenetic diversity in nontoxigenic O1 and O139 strains is observed, and most of the genes absent from nontoxigenic strains are clustered together in the N16961 genome. By comparing these toxigenic and nontoxigenic strains, we observed that the small chromosome of V. cholerae is quite conservative and stable, outside of the superintegron region. In contrast to the general stability of the genome, the superintegron demonstrates pronounced divergence among toxigenic and nontoxigenic strains. Additionally, sequence variation in virulence-related genes is found in nontoxigenic El Tor strains, and we speculate that these intermediate strains may have pathogenic potential should they acquire CTX prophage alleles and other gene clusters. This genome-wide comparison of toxigenic and nontoxigenic V. cholerae strains may promote understanding of clonal differentiation of V. cholerae and contribute to an understanding of the origins and clonal selection of epidemic strains.

scholarly journals Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 876
Author(s):  
Alexandra S. Abdelmanova ◽  
Arsen V. Dotsev ◽  
Michael N. Romanov ◽  
Olga I. Stanishevskaya ◽  
Elena A. Gladyr ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Artificial Selection ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Phenotypic Traits ◽  
Selection History ◽  
History Of ◽  
Efficient Breeding ◽  
Genomic Regions ◽  
Meat Type

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

scholarly journals Genomic diversity in European Spodoptera exigua multiple nucleopolyhedrovirus isolates

2014 ◽  
Vol 95 (10) ◽  
pp. 2297-2309 ◽  
Author(s):  
Julien Thézé ◽  
Oihana Cabodevilla ◽  
Leopoldo Palma ◽  
Trevor Williams ◽  
Primitivo Caballero ◽  
...  
Keyword(s):  
Spodoptera Exigua ◽  
Horizontal Transmission ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Functional Changes ◽  
Multiple Nucleopolyhedrovirus ◽  
Genome Analyses ◽  
Host Virus Interactions

Key virus traits such as virulence and transmission strategies rely on genetic variation that results in functional changes in the interactions between hosts and viruses. Here, comparative genomic analyses of seven isolates of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) with differing phenotypes were employed to pinpoint candidate genes that may be involved in host–virus interactions. These isolates obtained after vertical or horizontal transmission of infection in insects differed in virulence. Apart from one genome containing a piggyBac transposon, all European SeMNPV isolates had a similar genome size and content. Complete genome analyses of single nucleotide polymorphisms and insertions/deletions identified mutations in 48 ORFs that could result in functional changes. Among these, 13 ORFs could be correlated with particular phenotypic characteristics of SeMNPV isolates. Mutations were found in all gene functional classes and most of the changes we highlighted could potentially be associated with differences in transmission. The regulation of DNA replication (helicase, lef-7) and transcription (lef-9, p47) might be important for the establishment of sublethal infection prior to and following vertical transmission. Virus–host cell interactions also appear instrumental in the modulation of viral transmission as significant mutations were detected in virion proteins involved in primary (AC150) or secondary infections (ME35) and in apoptosis inhibition (IAP2, AC134). Baculovirus populations naturally harbour high genomic variation located in genes involved at different levels of the complex interactions between virus and host during the course of an infection. The comparative analyses performed here suggest that the differences in baculovirus virulence and transmission phenotypes involve multiple molecular pathways.

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.

SBA MCQs for the MRCS Part A

2012 ◽  
Author(s):  
Sri G. Thrumurthy ◽  
Tania Samantha De Silva ◽  
Zia Moinuddin ◽  
Stuart Enoch
Keyword(s):  
Clinical Case ◽  
Multiple Choice ◽  
Surgical Anatomy ◽  
Surgical Patients ◽  
Multiple Choice Questions ◽  
Basic Sciences ◽  
Self Assessment ◽  
High Level ◽  
Factual Recall ◽  
Selection Of

Specifically designed to help candidates revise for the MRCS exam, this book features 350 Single Best Answer multiple choice questions, covering the whole syllabus. Containing everything candidates need to pass the MRCS Part A SBA section of the exam, it focuses intensively on the application of basic sciences (applied surgical anatomy, physiology, and pathology) to the management of surgical patients. The high level of detail included within the questions and their explanations allows effective self-assessment of knowledge and quick identification of key areas requiring further attention. Varying approaches to Single Best Answer multiple choice questions are used, giving effective exam practice and guidance through revision and exam technique. This includes clinical case questions, 'positively-worded' questions, requiring selection of the most appropriate of relatively correct answers; 'two-step' or 'double-jump' questions, requiring several cognitive steps to arrive at the correct answer; as well as 'factual recall' questions, prompting basic recall of facts.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

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