Comparison of partial 23S rDNA sequences fromRhizobiumspecies

1997 ◽  
Vol 43 (6) ◽  
pp. 526-533 ◽  
Author(s):  
Mesfin Tesfaye ◽  
Daniel J. Petersen ◽  
F. Brian Holl
Keyword(s):  
Phylogenetic Relationships ◽  
Hypervariable Region ◽  
Nucleotide Sequences ◽  
23S Rrna ◽  
Strain Identification ◽  
Secondary Structure Analysis ◽  
16S Rdna Sequence Analysis ◽  
Rdna Sequences ◽  
Product Variation ◽  
Nodulation Specificity

A hypervariable region of Rhizobium 23S rDNA was amplified by polymerase chain reaction and phylogenetic relationships of several strains were determined by comparing nucleotide sequences of the amplified product. Variation in the 23S rDNA nucleotide sequences was consistent with phylogenetic relationships determined by host nodulation specificity and (or) 16S rDNA sequence analysis. Six strains representing three Rhizobium species (R. leguminosarum bv. trifolii, R. meliloti, and R. etli), and two strains each of Bradyrhizobium and Agrobacterium were clustered into five rDNA groups. Unique features identified by secondary structure analysis of the 23S rRNA sequenced region were consistent with the hypothesis that 23S rDNA could be used to design species- or strain-specific Rhizobium probes.Key words: Rhizobium, rDNA, strain identification, phylogeny.

Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences

1998 ◽  
Vol 209 (1-2) ◽  
pp. 75-83 ◽  
Author(s):  
Mats Wedin ◽  
Anders Tehler ◽  
Andrea Gargas
Keyword(s):  
Phylogenetic Relationships ◽  
Ssu Rdna ◽  
Rdna Sequences

scholarly journals ANÁLISE DA SIMILARIDADE DE SEQUÊNCIAS GÊNICAS DO ASCORBATO E DO LICOPENO EM ESPÉCIES VEGETAIS CULTIVADAS

2014 ◽  
Vol 6 (4) ◽  
pp. 09-20
Author(s):  
Ana Carolina P Malaman ◽  
Tais Lira Sevilha ◽  
Antonio Fluminhan
Keyword(s):  
Phylogenetic Relationships ◽  
Nucleotide Sequences ◽  
Similarity Matrix ◽  
Antioxidant Action ◽  
Degree Of Similarity

Bioinformatics has made possible the identificationand comparisonof nucleotide sequences responsible for the production of antioxidants compounds in plants by using genomic public accessdatabases and several applicationsable to alignsequencesfrom different species. The present study analyzed the nucleotide sequences ofthe genes for ascorbate and lycopene, known for its antioxidant action, in order to verify which species these substances havealready been identified as well as tocompare them through cladograms, observing the degree of similarity between thespeciesandtheirphylogenetic relationships.It was built the representation of similarity matrix from the genes, which might reflect the evolution of the remaining characters. This report shows the viability of the methodology, and providesa basis for more advanced studies about the phylogenetic relationships among the species

Phylogenetic relationships among species of Calyptogena (Bivalvia: Vesicomyidae) collected around Japan revealed by nucleotide sequences of mitochondrial genes

1995 ◽  
Vol 122 (3) ◽  
pp. 401-407 ◽  
Author(s):  
S. Kojima ◽  
R. Segawa ◽  
T. Kobayashi ◽  
T. Hashimoto ◽  
K. Fujikura ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nucleotide Sequences

scholarly journals Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the ‘next-generation’ Tree of Life

2019 ◽  
Vol 93 (3) ◽  
pp. 260-276 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
D.I. Hernández-Mena
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
28S Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Next Generation ◽  
Phylogenetic Classification ◽  
Rdna Sequences

AbstractDigenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.

scholarly journals Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences

2010 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcelo D Bechara ◽  
Márcio C Moretzsohn ◽  
Darío A Palmieri ◽  
Jomar P Monteiro ◽  
Maurício Bacci ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
5.8S Rdna ◽  
Rdna Sequences

scholarly journals RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

2000 ◽  
Vol 182 (17) ◽  
pp. 4719-4729 ◽  
Author(s):  
Elena Evguenieva-Hackenberg ◽  
Gabriele Klug
Keyword(s):  
Rhodobacter Capsulatus ◽  
23S Rrna ◽  
Recent Attempt ◽  
Rnase Iii ◽  
E Coli ◽  
Rdna Sequences ◽  
Intervening Sequences ◽  
Rna Maturation

ABSTRACT We provide experimental evidence for RNase III-dependent processing in helix 9 of the 23S rRNA as a general feature of many species in the alpha subclass of Proteobacteria(alpha-Proteobacteria). We investigated 12Rhodobacter, Rhizobium,Sinorhizobium, Rhodopseudomonas, andBartonella strains. The processed region is characterized by the presence of intervening sequences (IVSs). The 23S rDNA sequences between positions 109 and 205 (Escherichia coli numbering) were determined, and potential secondary structures are proposed. Comparison of the IVSs indicates very different evolutionary rates in some phylogenetic branches, lateral genetic transfer, and evolution by insertion and/or deletion. We show that the IVS processing inRhodobacter capsulatus in vivo is RNase III-dependent and that RNase III cleaves additional sites in vitro. While all IVS-containing transcripts tested are processed in vitro by RNase III from R. capsulatus, E. coli RNase III recognizes only some of them as substrates and in these substrates frequently cleaves at different scissile bonds. These results demonstrate the different substrate specificities of the two enzymes. Although RNase III plays an important role in the rRNA, mRNA, and bacteriophage RNA maturation, its substrate specificity is still not well understood. Comparison of the IVSs of helix 9 does not hint at sequence motives involved in recognition but reveals that the “antideterminant” model, which represents the most recent attempt to explain the E. coli RNase III specificity in vitro, cannot be applied to substrates derived from alpha-Proteobacteria.

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