PanOCT: Automated Clustering of Orthologs using Conserved Gene Neighborhood for Pan-Genomic Analysis of Bacterial Strains and Cl

SciVee ◽  
2012 ◽  
Author(s):  
Granger Sutton
Keyword(s):  
Genomic Analysis ◽  
Bacterial Strains ◽  
Gene Neighborhood ◽  
Conserved Gene

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

scholarly journals Lichenicola cladoniae gen. nov., sp. nov., a member of the family Acetobacteraceae isolated from an Antarctic lichen

2020 ◽  
Vol 70 (11) ◽  
pp. 5918-5925 ◽  
Author(s):  
Hyun-Ju Noh ◽  
Seung Chul Shin ◽  
Yerin Park ◽  
Ahyoung Choi ◽  
Kiwoon Baek ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Nitrate And Nitrite

Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569T, were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569T belong to the family Acetobacteraceae and the most closely related species are Gluconacetobacter takamatsuzukensis (96.1 %), Gluconacetobacter tumulisoli (95.9 %) and Gluconacetobacter sacchari (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569T are clearly distinguished from other genera in the family Acetobacteraceae by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569T do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569T possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 40.3–40.4 %), C18 : 1 2OH (22.7–23.7 %) and summed feature 2 (C14 : 0 3OH and/or C16 : 1 iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569T is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569T from other genera in the family Acetobacteraceae supporting the proposal of Lichenicola gen. nov., with the type species Lichenicola cladoniae sp. nov. (type strain, PAMC 26569T=KCCM 43315T=JCM 33604T).

scholarly journals Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

2020 ◽  
Vol 8 (9) ◽  
pp. 1441 ◽  
Author(s):  
Perrine Portier ◽  
Jacques Pédron ◽  
Géraldine Taghouti ◽  
Cécile Dutrieux ◽  
Marie-Anne Barny
Keyword(s):  
Host Plants ◽  
Plant Pathogens ◽  
Genomic Analysis ◽  
Taxonomic Status ◽  
Bacterial Strains ◽  
Freshwater Environment ◽  
New Host ◽  
Two New Species ◽  
Endemic Population ◽  
Prevalent Species

Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp.

Comparative genomic analysis of dwarf Vibrio myoviruses defines a conserved gene cluster for successful phage infection

2022 ◽  
Author(s):  
Dimitrios Skliros ◽  
Efthymios Karpouzis ◽  
Chrysanthi Kalloniati ◽  
Pantelis Katharios ◽  
Emmanouil Flemetakis
Keyword(s):  
Gene Cluster ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Phage Infection ◽  
Comparative Genomic ◽  
Conserved Gene

scholarly journals Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase

2019 ◽  
Vol 11 (7) ◽  
pp. 1959-1964 ◽  
Author(s):  
Jessica M Nelson ◽  
Duncan A Hauser ◽  
José A Gudiño ◽  
Yessenia A Guadalupe ◽  
John C Meeks ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
16S Rrna Sequence ◽  
Plant Microbe Interaction ◽  
Complete Genomes ◽  
Genes Encoding ◽  
Long Read ◽  
Vanadium Nitrogenase ◽  
Conserved Gene

Abstract Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant–microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.

scholarly journals Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

2022 ◽  
Vol 12 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Dayoung Kim ◽  
Hae-Yeong Kim
Keyword(s):  
Complete Genome ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Raw Milk ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Probiotic Properties ◽  
Bacterial Strains ◽  
Physiological Control ◽  
Wide Range

Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.

scholarly journals Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment

2021 ◽  
Vol 9 (8) ◽  
pp. 1736
Author(s):  
Jung-Yun Lee ◽  
Dong-Hun Lee ◽  
Dong-Hun Kim
Keyword(s):  
Amino Acid ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
General Function ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Average Amino Acid Identity ◽  
Iron Mine

Gram-stain-negative, strictly aerobic, non-spore-forming, non-motile, and rod-shaped bacterial strains, designated NC18T and NC20, were isolated from the sediment near-vertical borehole effluent originating 714 m below the subsurface located in the Soudan Iron Mine in Minnesota, USA. The 16S rRNA gene sequence showed that strains NC18T and NC20 grouped with members of the genus Martelella, including M. mediterranea DSM 17316T and M. limonii YC7034T. The genome sizes and G + C content of both NC18T and NC20 were 6.1 Mb and 61.8 mol%, respectively. Average nucleotide identity (ANI), the average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values were below the species delineation threshold. Pan-genomic analysis showed that NC18T, NC20, M. mediterranea DSM 17316T, M. endophytica YC6887T, and M. lutilitoris GH2-6T had 8470 pan-genome orthologous groups (POGs) in total. Five Martelella strains shared 2258 POG core, which were mainly associated with amino acid transport and metabolism, general function prediction only, carbohydrate transport and metabolism, translation, ribosomal structure and biogenesis, and transcription. The two novel strains had major fatty acids (>5%) including summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c, C16:0, C18:1 ω7c 11-methyl, C18:0, and summed feature 2 (C12:0 aldehyde and/or iso-C16:1 I and/or C14:0 3-OH). The sole respiratory quinone was uniquinone-10 (Q-10). On the basis of polyphasic taxonomic analyses, strains NC18T and NC20 represent novel species of the genus Martelella, for which the name Martelella soudanensis sp. nov. is proposed. The type strain is NC18T (=KTCT 82174T = NBRC 114661T).

Conservation of gene order in human microRNA-neighboring regions

Genome ◽  
2012 ◽  
Vol 55 (09) ◽  
pp. 701-704 ◽  
Author(s):  
Jianshu Chen ◽  
Wei Chen ◽  
Yudong Li
Keyword(s):  
Gene Order ◽  
Biological Function ◽  
Noncoding Rnas ◽  
Genomic Analysis ◽  
Unique Characteristic ◽  
Important Class ◽  
Human Mirnas ◽  
Genomic Architecture ◽  
Conserved Gene ◽  
Mouse Genomic

The biological function and evolution of microRNAs (miRNAs), an important class of noncoding regulatory genes, have attracted wide interest. However, their evolutionary impact on gene order rearrangements remains unknown. We examined the gene-order stability of miRNA-neighboring regions by a comparative human–mouse genomic analysis and found that the neighboring genes of human miRNAs tend to have a conserved gene order. This observation cannot be attributed to the functional bias of neighboring genes, and is a unique characteristic of miRNAs but not other noncoding RNAs. Our findings suggest that mammalian miRNAs stabilize the genomic architecture in evolution.

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