Taxonomy of the rhizobia

1992 ◽  
Vol 38 (6) ◽  
pp. 446-450 ◽  
Author(s):  
G. H. Elkan
Keyword(s):  
Genetic Relationships ◽  
Molecular Techniques ◽  
New Genera ◽  
Genetic Studies ◽  
Minimum Standards ◽  
Slow Growing ◽  
Taxonomic Characterization ◽  
Comprehensive Study

Extensive cross testing on a relatively few legume hosts led initially to a taxonomic characterization of rhizobia based on bacteria–plant cross–inoculation groups. This has gradually become less acceptable, and has been replaced by taxonomic groupings derived from numerical taxonomy, carbohydrate metabolism, antibiotic susceptiblities, serology, and various molecular techniques. It has long been recognized that there are two distinct groups of rhizobia based on growth rate. The fast-growing genus Rhizobium includes R. leguminosarum, R. meliloti, R. loti, R. galegae, R. tropici, and R. huakuii. The slow-growing genus Bradyrhizobium contains only one recognized species, B. japonicum. Two new genera have been recognized: Azorhizobium, with one recognized species (A. caulinadans), and Sinorhizobium, with two species (S. fredii and S. xinjiangensis). Genetic studies of both the fast- and slow-growing groups show unacceptably wide intrageneric and intergeneric diversity. Although there have been some elegant studies of some of the genetic relationships among rhizobia, overall there has (have) not been the comprehensive study(ies) needed to allow a conclusive taxonomic scheme. Because proposals for revision are accelerating, minimum standards have been proposed by the International Subcommittee for the Taxonomy of Rhizobium and Agrobacterium. Key words: Rhizobium taxonomy, classification of rhizobia, interrelationships of rhizobia.

scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

scholarly journals Prevalence of Hepatitis B in Blood Groups and Level of Education of Blood Donors in Al-Najaf Governorate

2021 ◽  
Vol 17 (4) ◽  
pp. 735-739
Author(s):  
Pritee Chunarkar Patil ◽  
Darshit Ashokkumar Patel ◽  
Vidya Sunil Tale
Keyword(s):  
Blood Donors ◽  
Dam Reservoir ◽  
Bacterial Composition ◽  
Biochemical Processes ◽  
Taxonomical Classification ◽  
Seasonal Analysis ◽  
Almost All ◽  
Taxonomic Characterization

Advancement in sequencing techniques and transformative progress in metagenomics provides an unprecedented platform for functional and taxonomic characterization of the enormous microbial diversity inhabiting and governing various biochemical processes of the freshwater sources. Metagenomic analysis of freshwater resources has led to the discovery and identification of novel microbial genes and an understanding of how microorganisms mediate energy and carbon. In this study, we report the taxonomical classification of bacterial sequences obtained from 6 dam reservoir sites in Pune city, Maharashtra, India. The analysis was performed using two different alignment tools: BLAST and Kaiju. The bacterial diversity was dominated by the presence of Vogecella indigofera, uncultured Proteobacterium, Wolinella Succinogenes, Chromobacterium violaceum, and Heliobacter billis. It was further observed that, despite an identical bacterial composition over various reservoir sites, there were nominal differences in the relative abundance of the inhabitant species. Almost all reservoirs were dominated by Vogecella indigofera (~29%) and uncultured Proteobacterium (~15%). A seasonal analysis performed using BLAST resulted in a number of species exclusive to the season and the site of their growth. A high proportion of unidentified sequences were also reported which demands sequential identification. The results obtained through BLAST and Kaiju, were significantly different, suggesting inconsistencies and inaccuracies in existing metagenomic reads comparison.

Collection and characterization of maize and upland rice populations cropped by poor farmers in the uplands of Panama's Azuero region

2008 ◽  
Vol 7 (02) ◽  
pp. 105-112
Author(s):  
B. E. Love ◽  
S. Dreisigacker ◽  
D. Spaner
Keyword(s):  
Genetic Diversity ◽  
Latin America ◽  
Upland Rice ◽  
Genetic Relationships ◽  
Phenotypic Differences ◽  
Crop Genetic Diversity ◽  
Maize Populations ◽  
Modern Varieties

The conservation of crop genetic resources is an international priority and requires the continued collection and characterization of farmer varieties. We collected and characterized maize and upland rice populations cropped by farmers in Panama's Azuero region. The objective of our study was to evaluate the crop genetic diversity of farmer varieties of maize and upland rice grown by poor farmers in Panama. We found that: (1) farmers' naming practices only partially corresponded to genetic relationships and were the strongest for rice populations; (2) farmers' classification of populations as ‘modern’ or ‘traditional’ was reflected in phenotypic differences; (3) Panamanian maize populations were molecularly distinct from populations collected elsewhere in Latin America; and (4) heterogeneous rice populations were common and heterogeneity was often due to admixture of recognized farmer varieties. Our results indicate that poor farmers in Panama continue to farm ‘traditional’ varieties that harbour genetic diversity of interest. There has, however, been substantial adoption of ‘modern’ varieties.

scholarly journals Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa

2020 ◽  
Vol 21 (18) ◽  
pp. 6681
Author(s):  
Simone Landi ◽  
Sergio Esposito
Keyword(s):  
Gene Family ◽  
Transcript Abundance ◽  
Sulfated Polysaccharides ◽  
Genetic Studies ◽  
Genomic Expression ◽  
Wide Range ◽  
Algal Genus ◽  
Commercial Applications

Caulerpa is an unusual algal genus from Caulerpaceae (Chlorophyta, Bryopsidales). Species from this family produce a wide range of metabolites suitable for biotechnology applications. Among these, sulfated polysaccharides (SPs) are often highly desirable for pharmaceutical and nutraceutical applications. Here, we provide a classification of sulfotransferases from Caulerpa; these important enzymes catalyze the nodal step for the biosynthesis of SPs. For this, we performed phylogenetic, genomic, expression analyses and prediction of the protein structure on sulfotransferases from Caulerpa. Sequences, domains and structures of sulfotransferases generally shared common characteristics with other plants and algae. However, we found an extensive duplication of sulfotransferase gene family, which is unique among the green algae. Expression analysis revealed specific transcript abundance in the pinnae and rachis of the alga. The unique genomic features could be utilized for the production of complex SPs, which require multiple and specific sulfation reactions. The expansion of this gene family in Caulerpaceae would have resulted in a number of proteins characterizing the unique SPs found in these algae. We provide a putative biosynthetic pathway of SPs, indicating the unique characteristics of this pathway in Caulerpa species. These data may help in the future selection of Caulerpa species for both commercial applications and genetic studies to improve the synthesis of valuable products from Caulerpa.

scholarly journals Genetic Studies of Selected „Black-Fruit” Hawthorns: Crataegus Nigra WALDST. et KIT., C. Pentagyna WALDST. et KIT. and C. Chlorosarca MAXIM.

2014 ◽  
Vol 10 (1) ◽  
pp. 23-29
Author(s):  
Viktor Kerényi-Nagy ◽  
Tamás Deák ◽  
Géza Kósa ◽  
Dénes Bartha
Keyword(s):  
Genetic Analysis ◽  
Related Species ◽  
Genetic Relationships ◽  
East Asian ◽  
Carpathian Basin ◽  
Genetic Studies ◽  
Infraspecific Variation ◽  
Maternal Parent

Abstract Genetic relationships of black-fruit hawthorns of the Carpathian basin have been investigated based on intergenic cpDNA sequences; first of all of the endemic Crataegus nigra and related species. Considerable infraspecific variation was detected in the East Asian taxon C. chlorosarca and some divergence in the Eurasian C. pentagyna. Based on the genetic analysis of investigated and reference psbA-trnH sequences, classification of sections Crataegus and Sanguineae is highly supported. From the studied taxa, C. pentagyna and C. monogyna was ordered to Sectio Crataegus, while C. nigra and .C. chlorosarca to Sectio Sanguineae. Based on our data, C. nigra can be considered as maternal parent of the investigated C. × degenii hybrids.

Applications of bulking in molecular characterization of plant germplasm: a critical review

2003 ◽  
Vol 1 (2-3) ◽  
pp. 161-167 ◽  
Author(s):  
Yong-Bi Fu
Keyword(s):  
Genetic Variation ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Low Frequency ◽  
Molecular Techniques ◽  
Technical Problems ◽  
Germplasm Identification ◽  
Plant Germplasm ◽  
Germplasm Collections

AbstractCharacterization of plant germplasm using molecular techniques is playing an increasingly important role in the management and utilization of plant genetic resources, but has its limitations in the screening of large numbers of accessions held in seed genebanks worldwide. Bulking individual plants from one accession or group to form a representative sample is a promising approach to widening the scope of a characterization, but it is not without technical problems in detecting genetic variation. This review was conducted to assess the technical pitfalls of bulking, and to evaluate the effectiveness of various bulking methods in the assessment of genetic variation and genetic relationships, and in the identification of plant germplasm. Clearly, some alleles, particularly those occurring at low frequency, may go undetected in a bulked sample, depending on the bulking methods and the molecular techniques used. As a result, genetic diversity estimates and genetic relationship inferences can be significantly biased. Germplasm identification may not be always reliable. Thus, it is imperative that the detection limit imposed by bulking be assessed for a newly initiated molecular germplasm characterization and bias be considered in interpretation of the resulting characterization data. Equally imperative is the need for continuous efforts of exploring efficient bulking procedures for the screening of large germplasm collections, particularly by the newly developed marker systems.

scholarly journals Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

2013 ◽  
Vol 94 (6) ◽  
pp. 1426-1434 ◽  
Author(s):  
Diego F. Quito-Avila ◽  
Philip M. Brannen ◽  
William O. Cline ◽  
Philip F. Harmon ◽  
Robert R. Martin
Keyword(s):  
Rna Virus ◽  
Genetic Relationships ◽  
Double Stranded Rna ◽  
Coding Regions ◽  
Genetic Features ◽  
The Usa ◽  
Highbush Blueberries ◽  
Southern Highbush

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3′ non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV.

scholarly journals Simple Sequence Repeat Identification and Endocarp Characterization of Olive Tree Accessions in a Tunisian Germplasm Collection

HortScience ◽  
2010 ◽  
Vol 45 (10) ◽  
pp. 1429-1436 ◽  
Author(s):  
Mahdi Fendri ◽  
Isabel Trujillo ◽  
Ahmed Trigui ◽  
María Isabel Rodríguez-García ◽  
Juan de Dios Alché Ramírez
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Olive Tree ◽  
Sequence Repeat ◽  
Olive Cultivars ◽  
Correspondence Factor Analysis ◽  
Simple Sequence

Most traditional olive-producing countries possess a diversified genetic patrimony in Olea europaea L. Since the emergence of modern olive growing system, the identification, classification, and conservation of autochthonous olive cultivars is a priority for these countries. In this work, a total of 84 accessions belonging to the “Boughrara”-Sfax olive germplasm collection located in Tunisia have been screened using a powerful set of eight simple sequence repeat markers (SSRs). The study revealed a high genetic variability among the collection and detected a total of 64 alleles. For better management of the mentioned germplasm bank, an improved classification of the entries, including new denominations, has been proposed. In addition, several cases of mislabeling, synonymy, and homonymy have been clarified. Genetic relationships among cultivars have been analyzed showing four major clusters. Finally, a correspondence factor analysis demonstrated that cultivars tend to cluster depending on their main use as oil or table olives. No clear clustering tendencies were observed when the geographical origin of cultivars was used as the criteria for the analysis. All results obtained by SSR screening and classification were in accordance with classification based on morphological traits of fruit endocarps.

scholarly journals AFLP Characterization of the Mexican Pineapple Germplasm Collection

2005 ◽  
Vol 130 (4) ◽  
pp. 575-579 ◽  
Author(s):  
Ermis Yanes Paz ◽  
Katia Gil ◽  
Laureano Rebolledo ◽  
Andrés Rebolledo ◽  
Daniel Uriza ◽  
...  
Keyword(s):  
Ivory Coast ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Molecular Classification ◽  
Ananas Comosus ◽  
Morphological Classification ◽  
Morphological Criteria

The Mexican pineapple germplasm collection represents the genetic diversity of cultivated pineapple [Ananas comosus (L.) Merr.] in that country and includes important genotypes from Hawaii, Ivory Coast, and Latin America. The collection has been partially characterized at the morphological level, but a molecular characterization has been lacking. With this aim, 39 genotypes of A. comosus var. comosus Coppens & Leal, two of A. comosus var. bracteatus (Lindl) Coppens & Leal, two of A. comosus var. ananassoides (Baker) Coppens & Leal, and three from the related genus Bromelia L. were analyzed with a total of 169 amplified fragment length polymorphism (AFLP) markers. A dendrogram representing the genetic relationships between these samples based on the AFLP results, showed a low level of diversity in the Mexican pineapple collection. In general, the molecular classification of the materials agreed well with the morphological classification. Several groups of genotypes showed distances of <0.03, whereas others thought to be similar based on morphological criteria were found to be distant. These results will allow more efficient use of the materials in the germplasm collection for breeding purposes and support the acquisition of genotypes that are scarce or lacking in the collection.

scholarly journals Prevalence of Hepatitis B in Blood Groups and Level of Education of Blood Donors in Al-Najaf Governorate

2021 ◽  
Vol 17 (4) ◽  
pp. 839-851
Author(s):  
Pritee Chunarkar Patil ◽  
Darshit Ashokkumar Patel ◽  
Vidya Sunil Tale
Keyword(s):  
Blood Donors ◽  
Dam Reservoir ◽  
Bacterial Composition ◽  
Biochemical Processes ◽  
Taxonomical Classification ◽  
Seasonal Analysis ◽  
Almost All ◽  
Taxonomic Characterization

Advancement in sequencing techniques and transformative progress in metagenomics provides an unprecedented platform for functional and taxonomic characterization of the enormous microbial diversity inhabiting and governing various biochemical processes of the freshwater sources. Metagenomic analysis of freshwater resources has led to the discovery and identification of novel microbial genes and an understanding of how microorganisms mediate energy and carbon. In this study, we report the taxonomical classification of bacterial sequences obtained from 6 dam reservoir sites in Pune city, Maharashtra, India. The analysis was performed using two different alignment tools: BLAST and Kaiju. The bacterial diversity was dominated by the presence of Vogecella indigofera, uncultured Proteobacterium, Wolinella Succinogenes, Chromobacterium violaceum, and Heliobacter billis. It was further observed that, despite an identical bacterial composition over various reservoir sites, there were nominal differences in the relative abundance of the inhabitant species. Almost all reservoirs were dominated by Vogecella indigofera (~29%) and uncultured Proteobacterium (~15%). A seasonal analysis performed using BLAST resulted in a number of species exclusive to the season and the site of their growth. A high proportion of unidentified sequences were also reported which demands sequential identification. The results obtained through BLAST and Kaiju, were significantly different, suggesting inconsistencies and inaccuracies in existing metagenomic reads comparison.

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