scholarly journals NeisseriaBase: a specialisedNeisseriagenomic resource and analysis platform

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1698
Author(s):  
Wenning Zheng ◽  
Naresh V.R. Mutha ◽  
Hamed Heydari ◽  
Avirup Dutta ◽  
Cheuk Chuen Siow ◽  
...  
Keyword(s):  
Web Application ◽  
Genetic Material ◽  
Gc Content ◽  
Genomic Analysis ◽  
Genome Comparison ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Diverse Range ◽  
Web Interfaces ◽  
The Web

Background.The gram-negativeNeisseriais associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for theNeisseriagenomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genusNeisseriaencompassing the complete and draft genomes of 15 pathogenic and commensalNeisseriaspecies.Methods.The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages.Results.Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227Neisseriagenomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing ofNeisseriagenomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis ofNeisseriastrains.Discussion.This user-friendly database not only provides access to a host of genomic resources onNeisseriabut also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested inNeisseriaresearch. This database is freely available athttp://neisseria.um.edu.my.

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

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 Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

2021 ◽  
Author(s):  
Jiaxin Yang ◽  
Guoxiong Hu ◽  
Guangwan Hu
Keyword(s):  
Endangered Species ◽  
Chloroplast Genome ◽  
Genome Size ◽  
Gc Content ◽  
Genomic Analysis ◽  
Single Copy ◽  
Comparative Genomic ◽  
Eurycorymbus Cavaleriei ◽  
Cp Genome ◽  
Relationship Of

Abstract Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisted of Aesculus chinensis and A. wangii, strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller across Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

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 Comparative Genomic Analysis of Limosilactobacillus Pontis Reveals Genetic Characteristics of High GC Content and Potential Niches Adaptations

2021 ◽  
Author(s):  
Qing Liu ◽  
Chen Liu ◽  
Weicheng Li ◽  
Wenjun Liu ◽  
Qing Liu
Keyword(s):  
Broiler Chickens ◽  
Gc Content ◽  
Genomic Analysis ◽  
Fermented Milk ◽  
Evolutionary Strategies ◽  
Comparative Genomic ◽  
Genetic Characteristics ◽  
Genomic Approach ◽  
Application Potential ◽  
Carbohydrate Enzymes

Abstract Limosilactobacillus pontis is a species of lactic acid bacteria (LAB) found in fermented milk, sourdough and broiler chickens gastrointestinal tract and so on. However, the evolutionary strategies and genomic characteristics of the species remain unknown, which limits its application. In this study, whole genome sequencing was combined with a comparative genomic approach to investigate genomic characteristics and evolutionary strategies of L. pontis; this includes three published genomic sequences and two strains isolated from fermented milk in Inner Mongolia, China. The mean genome size and GC content of L. pontis was 1.70 Mb and 53.06%, respectively. Within the LAB L. pontis has a high GC content. The phylogenetic tree based on 1,281 core genomes showed that strains from the same sources aggregated together in clusters. Genome information, average nucleotide identity values, and phylogenetic relationships amongst L. pontis from different sources indicated that strains have potential niche adaptability. Functional genomic aspects, GT2 and GT4 (glycosyltransferases, GTs) involved in the synthesis of cellulose and sucrose were the family with the largest number of carbohydrate enzymes in L. pontis, particularly strains isolated from fermented milk. It is worth mentioning that the ability of L. pontis to produce bacteriocin may increase its application potential. This study provides new insight into the genetic characteristics and potential niche adaptations of L. pontis.

scholarly journals Comparative Genomic Analysis of Bifidobacterium Catenulatum Reveal the Genetic Divergence of its Two Subspecies from Infant and Adult Gut

2021 ◽  
Author(s):  
Jiaqi Liu ◽  
Weicheng Li ◽  
Caiqing Yao ◽  
Jie Yu ◽  
Heping Zhang
Keyword(s):  
Genetic Divergence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Glycoside Hydrolases ◽  
Comparative Genomic ◽  
Carbohydrate Binding ◽  
Functional Difference ◽  
Carbohydrate Utilization ◽  
Carbohydrate Binding Modules ◽  
Genomic Studies

Abstract Background: Bifidobacterium catenulatum, which includes two subspecies that B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum are usually from infant and adult gut respectively, while the genomic studies of functional difference and genetic divergence in them have been rarely reported. In this study, we analyzed 16 B. catenulatum strains through comparative genomics, including two novel sequenced strains. Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated and confirmed their colonizing bias in infants and adults. Comparison of general genomic characteristics revealed that the two subspecies had significantly different genomic sizes but similar GC content. Functional annotations found that they peculiarly differ in utilization of carbohydrates and amino acid. Among them, we found that carbohydrate metabolism seems to play an important role in the divergence because of their carbohydrate-active enzymes (CAZyme) present two different clustering patterns. B. catenulatum subsp. kashiwanohense have functional genes that specifically adapted to the infant gut for glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51), which specifically participated in the metabolism of Human Milk Oligosaccharides (HMOs), and specific genes fuc that related to HMOs were also detected. While B. catenulatum subsp. catenulatum rich in GH3 and glycosyltransferases 4 (GT4) tended to metabolize plant-derived glycan that may help it metabolize more complex carbohydrates (eg. xylan) in the adult intestine. Conclusions: Our findings revealed genomic evidence of carbohydrate utilization bias which may be a key leading to the genetic divergence of two subspecies of B. catenulatum.

scholarly journals A large scale, multiple genome comparison of acidophilic Archaea (pH ≤ 5.0) extends our understanding of oxidative stress responses in polyextreme environments

2021 ◽  
Author(s):  
Gonzalo Neira ◽  
Eva Vergara ◽  
Diego Nahuel Cortez ◽  
David S. Holmes
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Large Scale ◽  
Genomic Analysis ◽  
Low Ph ◽  
Genome Comparison ◽  
Comparative Genomic ◽  
Acidophilic Bacteria ◽  
Acidophilic Archaea ◽  
Oxidative Stress Responses

Acidophilic Archaea thrive in anaerobic and aerobic low pH environments (<pH 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2·−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic Archaea with sequenced genomes. These organisms can be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what can this tell us about the evolution of these mechanisms in acidophilic Archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic Archaea and between acidophilic Archaea and acidophilic Bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in Archaea and possible Horizontal Gene Transfer (HGT) events.

scholarly journals Recombination Drives Emergence of Orf Virus Diversity: Evidence From the First Complete Genome of Indian Orf Virus and Comparative Genomic Analysis

2021 ◽  
Author(s):  
Debasis Nayak ◽  
Basanta Sahu ◽  
Prativa Majee ◽  
Ravi Singh ◽  
Niranjan Sahoo
Keyword(s):  
Complete Genome ◽  
Phylogenetic Trees ◽  
Small Ruminants ◽  
Gc Content ◽  
Genomic Analysis ◽  
Central India ◽  
Purifying Selection ◽  
Orf Virus ◽  
Comparative Genomic ◽  
Virus Diversity

Abstract Contagious pustular dermatitis is a disease that primarily infects small ruminants and has the zoonotic potential evoked by a Parapoxvirus, Orf virus (ORFV). This study evaluated an ORFV outbreak in goats that arose in Madhya Pradesh, a state of central India, during 2017 by constructing phylogenetic trees and unveiling its transboundary potential. Thereafter, the complete genome of an ORFV strain named Ind/MP has revealed the presence of 139,807bp nucleotide sequences, GC content 63.7%, 132 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 3,910bp. Evolutionary parameters such as selection pressure (θ=dN/dS), nucleotide diversity (π), etc., demonstrate the ORFV exhibit purifying selection. A total of forty recombination events were observed, out of which Ind/MP strains were engaged in twenty-one recombination events indicating this strain can recombine for the generation of new variants.

scholarly journals Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9171 ◽  
Author(s):  
Danial Nasr Azadani ◽  
Daiyuan Zhang ◽  
J. Robert Hatherill ◽  
David Silva ◽  
Jeffrey W. Turner
Keyword(s):  
Genome Sequencing ◽  
Large Subunit ◽  
Gc Content ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Single Locus ◽  
Comparative Genomic ◽  
Antibiotic Resistant ◽  
High Level ◽  
High Degree

Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even ‘conserved’ structural proteins (e.g., the large subunit terminase and portal proteins) were homologous in no more than half of the 32 phage genomes. These findings contribute to a growing body of literature devoted to understanding phage biology and diversity. We propose that this high degree of diversity limited the value of the single-locus and pangenome phylogenies. By contrast, the high degree of homology between phages larger than 100 kbp suggests that pangenome analyses of more similar phages is a viable method for assessing subclade diversity. Future work is focused on validating phiNASRA1 as a potential therapeutic agent to eradicate antibiotic-resistant E. faecalis infections in an animal model.

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