Genetic variability of the common nod gene in soybean bradyrhizobia isolated in Thailand and Japan

1996 ◽  
Vol 42 (12) ◽  
pp. 1209-1218 ◽  
Author(s):  
Tadashi Yokoyama ◽  
Shotaro Ando ◽  
Toshifumi Murakami ◽  
Hideo Imai
Keyword(s):  
Genetic Diversity ◽  
Bradyrhizobium Japonicum ◽  
Sequence Divergence ◽  
Gene Probe ◽  
Polymorphism Analysis ◽  
Dna Homology ◽  
Homology Groups ◽  
Phylogenetic Grouping ◽  
The Common ◽  
Bradyrhizobium Elkanii

To determine the taxonomic relationship between Thai soybean bradyrhizobia and soybean bradyrhizobia from other regions, a total of 62 Bradyrhizobium strains were isolated in Thailand. The genetic diversity of the strains was examined with reference to 46 Japanese and 15 USDA strains. The degree of sequence divergence in and around common nod gene regions of the 123 strains was estimated by restriction fragment length polymorphism analysis using the Bradyrhizobium japonicum USDA 110 common nodDYABC gene probe. The phylogenetic grouping of the strains resulted in four major clusters. Cluster 1 comprised the Japanese and USDA strains, which originated in temperate regions, whereas clusters 3 and 4 comprised the tropical Thai strains. Cluster 1 strains comprised the DNA homology groups I and Ia, and hence, were classified as B. japonicum. Cluster 2 strains were in the DNA homology group II, and hence, were classified as Bradyrhizobium elkanii. Clusters 3 and 4 strains, however, did not correspond to any known DNA homology groups. These results indicate that Thai soybean bradyrhizobia are distantly related to B. japonicum and B. elkanii.Key words: Bradyrhizobium japonicum, Bradyrhizobium elkanii, common nod gene, RFLP, genetic diversity.

Flavonoid-responsive nodY-lacZ expression in three phylogenetically different Bradyrhizobium groups

2008 ◽  
Vol 54 (5) ◽  
pp. 401-410 ◽  
Author(s):  
Tadashi Yokoyama
Keyword(s):  
Genetic Diversity ◽  
Bradyrhizobium Japonicum ◽  
Fragment Length Polymorphism ◽  
Gene Probe ◽  
Polymorphism Analysis ◽  
Lacz Expression ◽  
Nod Gene Induction ◽  
Reporter Strains ◽  
Bradyrhizobium Elkanii ◽  
Restriction Fragment Length

Previously, restriction fragment length polymorphism analysis using the nodD1YABC gene probe showed the genetic diversity of common nodD1ABC gene regions of Bradyrhizobium japonicum , Bradyrhizobium elkanii , and the Thai soybean Bradyrhizobium. The nodD1 sequences of representative strains of the 3 groups differed phylogenetically, suggesting that responses of NodD1 proteins of the 3 Bradyrhizobium groups to diverse flavonoids may differ. To confirm this hypothesis, 6 representative strains were chosen from the 3 Bradyrhizobium groups. Six reporter strains were constructed, all carrying the pZB32 plasmid, which contains a nod box and the nodY-lacZ fusion of B. japonicum USDA 110. Differences in nodY-lacZ expression among the strains in response to 37 flavonoid compounds at various concentrations were evaluated. Of those compounds, prunetin (4′,5-dihydroxy-7-methoxyisoflavone) and esculetin (6,7-dihydroxycoumarin) were identified as Bradyrhizobium group-specific nod gene inducers. Esculetin showed nod gene induction activities unique to Thai Bradyrhizobium strains. The levels of nodY-lacZ induction among B. japonicum and Thai Bradyrhizobium strains increased with increasing concentration of prunetin, whereas, those in B. elkanii strains did not.

Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp.nov.

1992 ◽  
Vol 38 (6) ◽  
pp. 501-505 ◽  
Author(s):  
L. D. Kuykendall ◽  
B. Saxena ◽  
T. E. Devine ◽  
S. E. Udell
Keyword(s):  
Type Strain ◽  
Homology Group ◽  
Dna Homology ◽  
Homology Groups ◽  
Hybridization Probes ◽  
Bradyrhizobium Elkanii ◽  
Group Ii ◽  
A New Species ◽  
Strain Usda ◽  
Soybean Nodulation

Fourteen randomly selected clones from cosmid libraries of Bradyrhizobium were used as hybridization probes in Southern blot analysis. Seven of the probes used were from strain USDA 83, a group II strain, and the other seven were from strain I-110, a group Ia strain. The 30 strains examined included 9 strains of Rj4-incompatible soybean bradyrhizobia. Considerable polynucleotide sequence dissimilarity between DNA homology groups was evidenced by striking differences in the number of hybridizing bands, except where the probe carried repetitive DNA. Predictable, simple restriction fragment length polymorphism differences were observed only within DNA homology groups. The previous description that 8 of 9 Rj4-incompatible strains belonged to DNA homology group II was verified. The new data, together with many previously documented differences, make it clear that the DNA homology group II organisms should be classified as a new species, for which the name Bradyrhizobium elkanii is proposed, and strain USDA 76 is designated the type strain. The ATCC number for the type strain is 49852. Key words: DNA:DNA hybridization, soybean, nodulation, bacteria, symbiosis, nitrogen fixation, host compatibility.

Compétition entre souches de Rhizobiaceae: mise en évidence de différents modes d'adhésion sur les racines de soja

1993 ◽  
Vol 39 (10) ◽  
pp. 982-986 ◽  
Author(s):  
C. Dolhem-Biremon ◽  
P. Mary ◽  
R. Tailliez
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Reference Strain ◽  
Competitive Behavior ◽  
Dna Homology ◽  
Bacterial Concentration ◽  
Homology Groups ◽  
Specific Recognition ◽  
Soybean Roots ◽  
Species Specific ◽  
Root Surfaces

Adhesion of 11 Rhizobiaceae strains on soybean roots was investigated. Whether these strains were able or not to nodulate soybean, they were found to adhere to these roots. Bacterial concentration above 1 × 1010 cells∙mL−1 was necessary to saturate root surfaces. Homologues and heterologous strains were used in mixed inoculation with Bradyrhizobium japonicum G49 StrR, used as reference strain in low number. Competition for adhesion was obtained at saturating concentrations of competitive strains. Only partial inhibition (< 55%) of the G49 StrR strain adhesion in the presence of heterologous strains was obtained, suggesting the occurrence of two modes of G49 StrR strain adhesion on the host roots: (i) a nonspecific adhesion of the B. japonicum and (ii) a specific adhesion of the B. japonicum or of strain G49 StrR. With homologous strains, inhibition of G49 StrR strain adhesion indicated a different competitive behavior between the four strains used belonging to the two DNA homology groups. Thus, the existence of species-specific recognition for all strains of B. japonicum, on soybean roots, remains to be confirmed.Key words: Rhizobiaceae, soybean, competition, adhesion, root.

Genetic diversity of island populations of the common shrew Sorex araneus

2007 ◽  
Vol 6 (1) ◽  
pp. 021-025
Author(s):  
Th.A. White ◽  
J.B. Searle
Keyword(s):  
Genetic Diversity ◽  
Common Shrew ◽  
Sorex Araneus ◽  
Island Populations ◽  
The Common ◽  
Common Shrew Sorex Araneus

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

scholarly journals Genetic diversity and evolution of hepatitis C virus – 15 years on

2004 ◽  
Vol 85 (11) ◽  
pp. 3173-3188 ◽  
Author(s):  
Peter Simmonds
Keyword(s):  
Genetic Diversity ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Human Liver ◽  
Large Population ◽  
Sequence Divergence ◽  
Selection Pressures ◽  
Host Interactions ◽  
Persistent Viruses ◽  
The Face

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus–host interactions may represent key components in establishing its ‘ecological niche’ in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

scholarly journals Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 155
Author(s):  
Kefena Effa ◽  
Sonia Rosenbom ◽  
Jianlin Han ◽  
Tadelle Dessie ◽  
Albano Beja-Pereira
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Sequence Divergence ◽  
Dna Polymorphisms ◽  
Base Pairs ◽  
Feral Horses ◽  
Domestic Horses ◽  
D Loop ◽  
Diversity Estimates

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

scholarly journals Genetic diversity of small-ruminant lentiviruses: characterization of Norwegian isolates of Caprine arthritis encephalitis virus

2006 ◽  
Vol 87 (3) ◽  
pp. 573-580 ◽  
Author(s):  
Britt Gjerset ◽  
Anne K. Storset ◽  
Espen Rimstad
Keyword(s):  
Genetic Diversity ◽  
Small Ruminant ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Encephalitis Virus ◽  
Surface Glycoprotein ◽  
Group Designation ◽  
Variable Regions ◽  
Caprine Arthritis Encephalitis Virus ◽  
Small Ruminant Lentiviruses

Small-ruminant lentiviruses (SRLVs), including Caprine arthritis encephalitis virus (CAEV) in goats and maedi-visna virus (MVV) in sheep, are lentiviruses that, despite overall similarities, show considerable genetic variation in regions of the SRLV genome. To gain further knowledge about the genetic diversity and phylogenetic relationships among field isolates of SRLVs occurring in geographically distinct areas, the full-length genomic sequence of a CAEV isolate (CAEV-1GA) and partial env sequences obtained from Norwegian CAEV-infected goats were determined. The genome of CAEV-1GA consisted of 8919 bp. Alignment studies indicated significant diversity from published SRLV sequences. Deletions and hypervariability in the 5′ part of the env gene have implications for the size of the proposed CAEV-1GA Rev protein and the encoded surface glycoprotein (SU). The variable regions in the C-terminal part of SU obtained from Norwegian CAEV isolates demonstrate higher sequence divergence than has been described previously for SRLVs. Phylogenetic analysis based on SU sequences gives further support for a unique group designation. The results described here reveal a distant genetic relationship between Norwegian CAEV and other SRLVs and demonstrate that there is more geographical heterogeneity among SRLVs than reported previously.

scholarly journals Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

2020 ◽  
Author(s):  
Mansoor Kodori ◽  
Zohreh Ghalavand ◽  
Abbas Yadegar ◽  
Gita Eslami ◽  
Masoumeh Azimirad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Disease Severity ◽  
Genetic Variants ◽  
Rflp Analysis ◽  
Clostridioides Difficile ◽  
Pcr Rflp ◽  
The Common ◽  
Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

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