scholarly journals New Insights into the Genetic Diversity of the Bacterial Plant Pathogen ‘Candidatus Liberibacter solanacearum’ as Revealed by a New Multilocus Sequence Analysis Scheme

2019 ◽  
Author(s):  
Ahmed Hajri ◽  
Pascaline Cousseau-Suhard ◽  
Pascal Gentit ◽  
Marianne Loiseau
Keyword(s):  
Sequence Data ◽  
Genetic Relationships ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
New Information ◽  
Analysis Scheme ◽  
History Of ◽  
Candidatus Liberibacter ◽  
Genetic Clusters ◽  
Clonal Population Structure

Abstract‘Candidatus Liberibacter solanacearum’ (Lso) has emerged as a serious threat on solanaceous and apiaceous crops worldwide. Five Lso haplotypes (LsoA, LsoB, LsoC, LsoD and LsoE) have been identified so far. To decipher genetic relationships between Lso strains, a MLSA study of seven housekeeping genes (acnA, atpD, ftsZ, glnA, glyA, gnd and groEL) was performed on a representative bacterial collection of 49 Lso strains. In all, 5415 bp spanning the seven loci were obtained from each of the 49 strains of our bacterial collection. Analysis of sequence data was consistent with a clonal population structure with no evidence of recombination. Phylogenies reconstructed from individual genes, and with concatenated data, were globally congruent with each other. In addition to the five highly supported and distinct genetic clusters, which correspond to the five established haplotypes, our phylogenetic data revealed the presence of a sixth haplotype, designated ‘LsoG’. This new haplotype is currently represented by two strains from France which had distinct sequences in four out of the seven tested housekeeping genes. Altogether, the data presented here provide new information regarding the genetic structure of Lso and the evolutionary history of the haplotypes defined within this bacterial species.

scholarly journals A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

2009 ◽  
Vol 75 (16) ◽  
pp. 5410-5416 ◽  
Author(s):  
Gabriele Margos ◽  
Stephanie A. Vollmer ◽  
Muriel Cornet ◽  
Martine Garnier ◽  
Volker Fingerle ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Lyme Borreliosis ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Species Status ◽  
Borrelia Garinii ◽  
Analysis Scheme ◽  
History Of

ABSTRACT Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

scholarly journals Multilocus sequence analysis and comparative evolution of virulence-associated genes and housekeeping genes of Clostridium difficile

Microbiology ◽  
2005 ◽  
Vol 151 (10) ◽  
pp. 3171-3180 ◽  
Author(s):  
Ludovic Lemée ◽  
Ingrid Bourgeois ◽  
Elodie Ruffin ◽  
Anne Collignon ◽  
Jean-François Lemeland ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Clostridium Difficile ◽  
Genetic Relationships ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Binary Toxin ◽  
Toxin A ◽  
Toxin Genes ◽  
Colonization Factor ◽  
Clonal Population Structure

A multilocus sequence analysis of ten virulence-associated genes was performed to study the genetic relationships between 29 Clostridium difficile isolates of various origins, hosts and clinical presentations, and selected from the main lineages previously defined by multilocus sequence typing (MLST) of housekeeping genes. Colonization-factor-encoding genes (cwp66, cwp84, fbp68, fliC, fliD, groEL and slpA), toxin A and B genes (tcdA and tcdB), and the toxin A and B positive regulator gene (tcdD) were investigated. Binary toxin genes (cdtA and cdtB) were also detected, and internal fragments were sequenced for positive isolates. Virulence-associated genes exhibited a moderate polymorphism, comparable to the polymorphism of housekeeping genes, whereas cwp66 and slpA genes appeared highly polymorphic. Isolates recovered from human pseudomembranous colitis cases did not define a specific lineage. The presence of binary toxin genes, detected in five of the 29 isolates (17 %), was also not linked to clinical presentation. Conversely, toxigenic A−B+ isolates defined a very homogeneous lineage, which is distantly related to other isolates. By clustering analysis, animal isolates were intermixed with human isolates. Multilocus sequence analysis of virulence-associated genes is consistent with a clonal population structure for C. difficile and with the lack of host specificity. The data suggest a co-evolution of several of the virulence-associated genes studied (including toxins A and B and the binary toxin genes) with housekeeping genes, reflecting the genetic background of C. difficile, whereas flagellin, cwp66 and slpA genes may undergo recombination events and/or environmental selective pressure.

scholarly journals Clonal Population Structure of Pseudomonas stutzeri, a Species with Exceptional Genetic Diversity

2001 ◽  
Vol 183 (2) ◽  
pp. 736-744 ◽  
Author(s):  
Núria Rius ◽  
M. Carme Fusté ◽  
Caterina Guasp ◽  
Jorge Lalucat ◽  
José G. Lorén
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Bacterial Species ◽  
Pseudomonas Stutzeri ◽  
Null Alleles ◽  
Enzyme Electrophoresis ◽  
Single Strain ◽  
Multilocus Enzyme Electrophoresis ◽  
Clonal Population Structure

ABSTRACT Genetic diversity and genetic relationships among 42Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, thisP. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (IA ) for the P. stutzeri strains analyzed was 1.10. The IA values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.

scholarly journals Multilocus Sequence Type System for the Plant Pathogen Xylella fastidiosa and Relative Contributions of Recombination and Point Mutation to Clonal Diversity

2005 ◽  
Vol 71 (12) ◽  
pp. 8491-8499 ◽  
Author(s):  
Mark Scally ◽  
Erin L. Schuenzel ◽  
Richard Stouthamer ◽  
Leonard Nunney
Keyword(s):  
Point Mutation ◽  
Plant Pathogen ◽  
Recombination Rate ◽  
Sequence Data ◽  
Xylella Fastidiosa ◽  
Bacterial Species ◽  
Type System ◽  
Clonal Diversity ◽  
Housekeeping Genes ◽  
Bacterial Strains

ABSTRACT Multilocus sequence typing (MLST) identifies and groups bacterial strains based on DNA sequence data from (typically) seven housekeeping genes. MLST has also been employed to estimate the relative contributions of recombination and point mutation to clonal divergence. We applied MLST to the plant pathogen Xylella fastidiosa using an initial set of sequences for 10 loci (9.3 kb) of 25 strains from five different host plants, grapevine (PD strains), oleander (OLS strains), oak (OAK strains), almond (ALS strains), and peach (PP strains). An eBURST analysis identified six clonal complexes using the grouping criterion that each member must be identical to at least one other member at 7 or more of the 10 loci. These clonal complexes corresponded to previously identified phylogenetic clades; clonal complex 1 (CC1) (all PD strains plus two ALS strains) and CC2 (OLS strains) defined the X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. sandyi clades, while CC3 (ALS strains), CC4 (OAK strains), and CC5 (PP strains) were subclades of X. fastidiosa subsp. multiplex. CC6 (ALS strains) identified an X. fastidiosa subsp. multiplex-like group characterized by a high frequency of intersubspecific recombination. Compared to the recombination rate in other bacterial species, the recombination rate in X. fastidiosa is relatively low. Recombination between different alleles was estimated to give rise to 76% of the nucleotide changes and 31% of the allelic changes observed. The housekeeping loci holC, nuoL, leuA, gltT, cysG, petC, and lacF were chosen to form the basis of a public database for typing X. fastidiosa (www.mlst.net ). These loci identified the same six clonal complexes using the strain grouping criterion of identity at five or more loci with at least one other member.

scholarly journals Algerian Olive Germplasm and Its Relationships with the Central-Western Mediterranean Varieties Contributes to Clarify Cultivated Olive Diversification

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 678
Author(s):  
Kamel Atrouz ◽  
Ratiba Bousba ◽  
Francesco Paolo Marra ◽  
Annalisa Marchese ◽  
Francesca Luisa Conforti ◽  
...  
Keyword(s):  
Mediterranean Basin ◽  
Genetic Relationships ◽  
Olive Tree ◽  
Mediterranean Area ◽  
Western Mediterranean ◽  
Central Mediterranean ◽  
Western Mediterranean Basin ◽  
New Information ◽  
Mediterranean History ◽  
New Synonymy

Olive tree with its main final product, olive oil, is an important element of Mediterranean history, considered the emblematic fruit of a civilization. Despite its wide diffusion and economic and cultural importance, its evolutionary and phylogenetic history is still difficult to clarify. As part of the Mediterranean basin, Algeria was indicated as a secondary diversification center. However, genetic characterization studies from Maghreb area, are currently underrepresented. In this context, we characterized 119 endemic Algerian accessions by using 12 microsatellite markers with the main goal to evaluate the genetic diversity and population structure. In order to provide new insights about the history of olive diversification events in the Central-Western Mediterranean basin, we included and analyzed a sample of 103 Italian accessions from Sicily and, a set of molecular profiles of cultivars from the Central-Western Mediterranean area. The phylogenetic investigation let us to evaluate genetic relationships among Central-Mediterranean basin olive germplasm, highlight new synonymy cases to support the importance of vegetative propagation in the cultivated olive diffusion and consolidate the hypothesis of more recent admixture events occurrence. This work provided new information about Algerian germplasm biodiversity and contributed to clarify olive diversification process.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

scholarly journals Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Julia Lanner ◽  
Fabian Gstöttenmayer ◽  
Manuel Curto ◽  
Benoît Geslin ◽  
Katharina Huchler ◽  
...  
Keyword(s):  
Cluster Formation ◽  
Invasion History ◽  
European Continent ◽  
Multiple Introductions ◽  
Wild Bee ◽  
Invasion Stage ◽  
Middle Europe ◽  
History Of ◽  
Genetic Clusters ◽  
Colonization Dynamics

Abstract Background Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts. Result To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east–west differentiations in Middle-Europe. Conclusion We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.

scholarly journals The Ocular Gene Delivery Landscape

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1135
Author(s):  
Bhubanananda Sahu ◽  
Isha Chug ◽  
Hemant Khanna
Keyword(s):  
Gene Therapy ◽  
Genetic Diseases ◽  
Gene Therapies ◽  
Advantages And Disadvantages ◽  
Fda Approval ◽  
New Information ◽  
Efficient Delivery ◽  
Delivery Routes ◽  
History Of ◽  
Different Parts

The eye is at the forefront of developing therapies for genetic diseases. With the FDA approval of the first gene-therapy drug for a form of congenital blindness, numerous studies have been initiated to develop gene therapies for other forms of eye diseases. These examinations have revealed new information about the benefits as well as restrictions to using drug-delivery routes to the different parts of the eye. In this article, we will discuss a brief history of gene therapy and its importance to the eye and ocular delivery landscape that is currently being investigated, and provide insights into their advantages and disadvantages. Efficient delivery routes and vehicle are crucial for an effective, safe, and longer-lasting therapy.

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