scholarly journals Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sungmi Choi ◽  
Min-gyung Baek ◽  
Myung-Jun Chung ◽  
Sanghyun Lim ◽  
Hana Yi
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Strain Diversity ◽  
Genomic Analyses ◽  
High Level ◽  
Encoding Genes ◽  
Probiotic Activity ◽  
Bacteriocin Genes ◽  
Ancestral Type

AbstractLactiplantibacillus plantarum, previously named “Lactobacillus plantarum,” is found in a wide variety of environments exhibiting a high level of intraspecies genetic diversity. To investigate the strain diversity, we performed comparative genomic analyses of the 54 complete genome sequences. The results revealed that L. plantarum subsp. plantarum was split into three lineages, A, B and C. Of the genes beneficial for probiotic activity, only those associated with the biosynthesis of plantaricin (Pln), an L. plantarum-specific bacteriocin, were found to be significantly different among the lineages. The genes related to the biosynthesis of plnE/F were conserved throughout the three lineages, whereas the outgroups did not possess any Pln-producing genes. In lineage C, the deepest and ancestral type branch, plnE/F genes, were well conserved. In lineage B, loss of gene function was observed due to mobile elements in the pln loci. In lineage A, most strains were predicted to produce more than one type of Pln by possessing diverse Pln-encoding genes. These results showed the presence of functional diversity arising from the trifurcating evolution in L. plantarum subsp. plantarum and demonstrated that Pln is an indicator for differentiating the three lineages.

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals Current Progress in Evolutionary Comparative Genomics of Great Apes

2021 ◽  
Vol 12 ◽  
Author(s):  
Aisha Yousaf ◽  
Junfeng Liu ◽  
Sicheng Ye ◽  
Hua Chen
Keyword(s):  
Evolutionary History ◽  
Comparative Genomic ◽  
Great Ape ◽  
Structural Variations ◽  
Genome Sequences ◽  
New Genes ◽  
Genomic Analyses ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Human Specific

The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.

scholarly journals Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

2017 ◽  
Vol 35 (8) ◽  
pp. 725-731 ◽  
Author(s):  
Robert M Bowers ◽  
◽  
Nikos C Kyrpides ◽  
Ramunas Stepanauskas ◽  
Miranda Harmon-Smith ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Marker Gene ◽  
Comparative Genomic ◽  
Archaeal Diversity ◽  
Genome Sequences ◽  
Assembly Quality ◽  
Metagenomic Sequence ◽  
Minimum Information ◽  
A Genome ◽  
Genomic Analyses

AbstractWe present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

scholarly journals Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 95
Author(s):  
Yan Jia ◽  
Bo Yang ◽  
Paul Ross ◽  
Catherine Stanton ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sugar Metabolism ◽  
Comparative Genomic ◽  
Related Factors ◽  
Genomic Analyses ◽  
Human Vagina ◽  
New Ideas ◽  
Comparative Genomics Analysis ◽  
Lactobacillus Mucosae ◽  
First Time

The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

scholarly journals Draft Genome Sequences of Elsinoë fawcettii and Elsinoë australis Causing Scab Diseases on Citrus

2020 ◽  
Vol 33 (2) ◽  
pp. 135-137 ◽  
Author(s):  
Gnanendra Shanmugam ◽  
Junhyun Jeon ◽  
Jae-Wook Hyun
Keyword(s):  
Ab Initio ◽  
Host Range ◽  
Draft Genome ◽  
Phytopathogenic Fungi ◽  
Comparative Genomic ◽  
Sequence Information ◽  
Genome Sequences ◽  
High Quality ◽  
Genomic Analyses ◽  
Genome Sequence Information

Elsinoë fawcettii and E. australis (phylum Ascomycota) are phytopathogenic fungi causing scab diseases on citrus plants. We report here the high-quality draft genome sequences and ab initio gene predictions of two E. fawcettii strains and one E. australis strain, which differ in their host range. This genome sequence information will provide valuable resources to underpin genomic attributes for determining host range through comparative genomic analyses of citrus scab fungi.

scholarly journals Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chen ◽  
Chao-Yue Cui ◽  
Jun-Jun Yu ◽  
Qian He ◽  
Xiao-Ting Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bacterial Species ◽  
Sequence Divergence ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Phenotypic Variance ◽  
Evolutionary Analysis ◽  
Acinetobacter Species ◽  
Recent Emergence ◽  
High Level

Abstract Background The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infections caused by multidrug-resistant Gram-negative and Gram-positive pathogens. Although tet(X) has been found in various bacterial species, less is known about phylogeographic distribution and phenotypic variance of different genetic variants. Methods Herein, we conducted a multiregional whole-genome sequencing study of tet(X)-positive Acinetobacter isolates from human, animal, and their surrounding environmental sources in China. The molecular and enzymatic features of tet(X) variants were characterized by clonal expression, microbial degradation, reverse transcription, and gene transfer experiments, while the tet(X) genetic diversity and molecular evolution were explored by comparative genomic and Bayesian evolutionary analyses. Results We identified 193 tet(X)-positive isolates from 3846 samples, with the prevalence ranging from 2.3 to 25.3% in nine provinces in China. The tet(X) was broadly distributed in 12 Acinetobacter species, including six novel species firstly described here. Besides tet(X3) (n = 188) and tet(X4) (n = 5), two tet(X5) variants, tet(X5.2) (n = 36) and tet(X5.3) (n = 4), were also found together with tet(X3) or tet(X4) but without additive effects on tetracyclines. These tet(X)-positive Acinetobacter spp. isolates exhibited 100% resistance rates to tigecycline and tetracycline, as well as high minimum inhibitory concentrations to eravacycline (2–8 μg/mL) and omadacycline (8–16 μg/mL). Genetic analysis revealed that different tet(X) variants shared an analogous ISCR2-mediated transposon structure. The molecular evolutionary analysis indicated that Tet(X) variants likely shared the same common ancestor with the chromosomal monooxygenases that are found in environmental Flavobacteriaceae bacteria, but sequence divergence suggested separation ~ 9900 years ago (7887 BC), presumably associated with the mobilization of tet(X)-like genes through horizontal transfer. Conclusions Four tet(X) variants were identified in this study, and they were widely distributed in multiple Acinetobacter spp. strains from various ecological niches across China. Our research also highlighted the crucial role of ISCR2 in mobilizing tet(X)-like genes between different Acinetobacter species and explored the evolutionary history of Tet(X)-like monooxygenases. Further studies are needed to evaluate the clinical impact of these mobile tigecycline resistance genes.

scholarly journals Genomic Features and Comparative Genomic Analysis of novel Bacillus glycinifermentans strain JRCGR-1

2021 ◽  
Author(s):  
Asad Karim ◽  
poirot olivier ◽  
Ambrina Khatoon ◽  
Matthieu Legendre
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Public Database ◽  
Genome Sequences ◽  
Genomic Features ◽  
The Public ◽  
Comparative Genomics Analysis ◽  
High Level

Abstract To the best of our knowledge, only six B. glycinifermentans sp. genome sequences are available in the public database. Here, we performed genome sequencing and comparative genomics analysis of B. glycinifermentans strain JRCGR-1. Cluster analysis of strain JRCGR-1 genes showed that 92.6% of genes were present in the orthogroups and 7.4% genes were not assigned to any group. The pangenome size was calculated at 8329 genes and presented an open genome characteristic. Phylogeny based on the pan and core genome demonstrated that all the B. glycinifermentans strains belong to the same clade. The strain JRCGR-1, ANI, TETRA and DDH values were in the range of 96.1-99.04%, 0.996-997, 73.5–84.7%, respectively. The strain JRCGR genome exhibits a high level of synteny with multiple locations in B. sonorensis sp. and B. licheniformis sp. The finding of the current study provides knowledge that facilitates a better understanding of this at the genomic level.

scholarly journals Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas

2017 ◽  
Vol 5 (45) ◽  
Author(s):  
Hui-Min Chung ◽  
Tom D’Elia ◽  
Joseph F. Ross ◽  
Samuel M. Alvarado ◽  
Molly-Catherine Brantley ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Complete Genome ◽  
Soil Samples ◽  
Comparative Genomic ◽  
Gene Conservation ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Analyses

ABSTRACT We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using Mycobacterium smegmatis mc2155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

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