Phylogenetic and genomic relationships in the genus Glycine Willd. based on sequences from the ITS region of nuclear rDNA

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 57-68 ◽  
Author(s):  
Krishna P. Kollipara ◽  
Ram J. Singh ◽  
Theodore Hymowitz
Keyword(s):  
Sequence Variation ◽  
Glycine Soja ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Single Nucleotide ◽  
Nucleotide Sequence Variation ◽  
Genomic Relationships ◽  
Its1 And Its2

Phylogenetic relationships among all 18 species of the genus Glycine were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Pairwise sequence divergence values ranged from 0.2% (a single nucleotide) between Glycine max and Glycine soja to 8.6% between Glycine hirticaulis and Glycine falcata. The length of the ITS1 and ITS2 sequences ranged from 215 to 238 nucleotides and from 205 to 222 nucleotides, respectively, and that of 5.8S was 168 nucleotides across all the species. Phylogenetic analyses of the ITS region clearly resolved all the genomic groups that were established previously based on cytogenetic and biochemical studies. Based on this study, we assign new genome symbols: HH to Glycine arenaria, H1H1 to Glycine hirticaulis, H2H2 to Glycine pindanica, II to Glycine albicans, and I1I1 to Glycine lactovirens. Parsimony analysis of the entire ITS region, using subgenus Soja as outgroup, resulted in a trichotomy consisting of the clades: G. falcata (F genome), Glycine cyrtoloba and Glycine curvata (C genome), and all other species (A, B, D, E, H, and I genomes) of the subgenus Glycine.Key words: Glycine spp., soybean, genomes, ITS region, rDNA.

scholarly journals Identification of species in the genus Nitraria L. (Nitrariaceae) based on nucleotide variability of nuclear ribosomal DNA

2020 ◽  
Vol 24 (5) ◽  
pp. 481-488
Author(s):  
T. A. Poliakova ◽  
E. V. Banaev ◽  
M. A. Tomoshevich
Keyword(s):  
Ribosomal Dna ◽  
Gc Content ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Single Nucleotide Deletion ◽  
Nucleotide Variability ◽  
Its1 And Its2

Intragenomic polymorphism of ITS1 and ITS2 of nuclear ribosomal DNA sequences was analysed in 33 samples belonging to the Nitraria species N. schoberi, N. sibirica, and N. komarovii. The nucleotide variability of the ITS region was detected in the Nitraria species as single-nucleotide substitutions (mainly transitions) and single-nucleotide deletion. Information about the nucleotide variability of fragments is given for the first time by us. The ITS1-5.8S-ITS2 region contained 17 phylogenetically informative single-nucleotide polymorphisms. Eleven single-nucleotide substitutions (transitions, C/T) were detected in ITS1. The ITS2 spacer contained 273–274 bp and was more conservative. A total of 5 phylogenetically informative single-nucleotide polymorphisms (4 transitions: C/T, G/A, one transversion: G/C), one single-nucleotide deletion (T/–) were detected in ITS2. The average GC content was 61.5 %. The GC content was lower in N. sibirica (59.2 %) than in N. schoberi and N. komarovii (62.7 %). It has been shown that the shorter ITS2 is a suitable molecular marker separating these species, due to the low interspecific variability and simultaneous available intraspecific variability. Phylogenetic ML and BI trees constructed separately for the ITS1 and ITS2 spacers, as well as separately for the full-size ITS region and the ITS2 spacer, were congruent. The results obtained on the intraspecific differentiation of N. sibirica revealed two main ribotypes among the samples of this species: the main Siberian sibirica-ribotype and the main Kazakh sibiricaribotype. Geographical features of the distribution of N. sibirica ribotypes, as well as the presence of significant differences between the main Siberian and Kazakh sibirica-ribotypes (3 single-nucleotide substitutions) indicated significant inter-population differences and taxonomic heterogeneity of N. sibirica. Most likely, the processes of homogenization of nuclear ribosomal DNA of N. sibirica samples, the origin of which is associated with hybridization and speciation, are currently continuing.

ORIGIN AND RELATIONSHIPS OF ALPINIA GALANGA (ZINGIBERACEAE) BASED ON MOLECULAR DATA

2000 ◽  
Vol 57 (1) ◽  
pp. 9-37 ◽  
Author(s):  
A. RANGSIRUJI ◽  
M. F. NEWMAN ◽  
Q. C. B. CRONK
Keyword(s):  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Sister Relationship ◽  
Important Species ◽  
Alpinia Galanga ◽  
Decay Index ◽  
Molecular Phylogenetic

Alpinia galanga is an important species cultivated as a culinary spice and is the type species of the genus. It is hence a member of sect. Alpinia subsect. Alpinia (with non-tubular bracteoles). However, molecular phylogenetic analyses suggest that A. galanga is closely related to A. nigra in sect. Allughas (with tubular bracteoles). This clade, which includes A. conchigera, is strongly supported with a bootstrap value (BS) of 100% and a decay index (DI) of >+6. These results are based on the internal transcribed spacer (ITS) region of the 18S–25S nuclear ribosomal DNA. The region (405–423bp) was sequenced from 17 accessions representing 16 taxa of Zingiberaceae, including 15 species of Alpinia and one outgroup. The sequence divergence ranged from 0.5 to 15.6% among the ingroup and from 10.1 to 13.3% between the ingroup and the outgroup. The results also strongly support the sister relationship of A. rafflesiana and A. javanica in section Allughas (BS=100%, DI=>+6), thus the whole section is paraphyletic. Section Alpinia subsect. Catimbium is monophyletic (BS=100%, DI=+5). On the other hand, sect. Alpinia subsect. Alpinia is paraphyletic (BS=100%, DI=>+6) with respect to sect. Alpinia subsect. Catimbium. The results from a phylogenetic analysis of a subset of the taxa using the spacer between trnL (UAA) 3′ exon and trnF (GAA) of chloroplast DNA confirmed the position of A. galanga in sect. Allughas. It appears that A. galanga has evolved within sect. Allughas and the absence of tubular bracteoles is a convergence with sect. Alpinia, possibly as a result of evolution under domestication.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Molecular phylogeny of the tribe Anthospermeae (Rubiaceae): Systematic and biogeographic implications

2001 ◽  
Vol 14 (2) ◽  
pp. 231 ◽  
Author(s):  
Cajsa L. Anderson ◽  
Johan H. E. Rova ◽  
Lennart Andersson
Keyword(s):  
Its Region ◽  
Plastid Dna ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Ancestral Area ◽  
Nucleotide Sequence Variation ◽  
North Eastern ◽  
One Step

Phylogeny of the tribe Anthospermeae is estimated on the basis of nucleotide sequence variation in the ITS region (nuclear ribosomal DNA) and the rps16 intron (plastid DNA). It is concluded that it is dubious whether the tribe is monophyletic including Carpacoce. If Carpacoce does belong to the tribe, then it is the sister group of all other genera. There is no support for the traditional subdivision of the tribe into three subtribes. Anthospermum, Galopina, Nenax and Phyllis form one strongly supported subclade. Coprosma, Durringtonia, Leptostigma, Nertera, Normandia, Opercularia and Pomax form another subclade in all most parsimonious trees, but this subclade lacks jackknife support. Opercularia and Pomax, referred to the subtribe Operculariinae, form a basal grade of this second group. However, trees on which Operculariinae are monophyletic are only one step longer than the most parsimonious ones. Normandia is deeply nested within Coprosma. The subdivision of Coprosma into two subgenera is shown to be artificial. It is suggested that the ancestral area of Anthospermeae is Africa, and that the group was spread by long-distance dispersal to north-eastern Antarctica. It is further suggested that occurrences in Hawaii, Tristan da Cunha, and America are due to long-distance dispersal at a time much later than primary cladogenesis.

scholarly journals Foeniculum sanguineum Triano & A. Pujadas (Apiaceae) new species from the South-Western Mediterranean Region

2017 ◽  
Vol 40 ◽  
pp. 71
Author(s):  
Antonio J. Pujadas Salvà ◽  
Enrique Triano Muñoz ◽  
Josefa Anaya ◽  
Manuel Grande ◽  
César Raposo ◽  
...  
Keyword(s):  
New Species ◽  
Mediterranean Region ◽  
Phylogenetic Analyses ◽  
Diploid Species ◽  
Sequence Divergence ◽  
Western Mediterranean ◽  
Nuclear Ribosomal Dna ◽  
Rbcl Gene ◽  
The South ◽  
Foeniculum Vulgare

English. Foeniculum sanguineum Triano & A. Pujadas, sp. nov., from the south western Mediterranean Region (Spain & Morocco) is described. Its characterization and a comparative study with the related species Foeniculum vulgare Mill., has been carried out through morphological, cytological, chemical and molecular analysis. F. sanguineum is distinguished primarily for its red petals, pink pollen in fresh, and red stylopod. It is a diploid species (2n= 22). A high proportion of limonene and piperitenone oxide (absent in F. vulgare) has been found in the essential oil composition of the dry fruits of F. sanguineum and a high amount (about 50 %) of α-phellandrene in its roots and stems. Phylogenetic analyses were performed using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) and the chloroplast rbcL gene sequences. ITS analysis supports the existence of the new species, while revealing sequence divergence both at the intraspecific and at the interspecific levels. A Single-nucleotide-polymorphism (SNP) sequence divergence found in the slow evolving chloroplast gene provided additional support for the novel species characterization, for which the name Foeniculum sanguineum is proposed.Español.  Se describe Foeniculum sanguineum Triano & A. Pujadas, sp. nov., del suroeste de la Región Mediterránea (España y Marruecos). Para su caracterización se ha realizado el análisis morfológico, citológico, fitoquímico y molecular. Se ha llevado a cabo el studio comparativo con Foeniculum vulgare Mill. La nueva especie F. sanguineum se distingue principalmente por sus pétalos rojos, polen rosado en fresco y por su estilopodio rojo. Es una especie diploide (2n= 22). Se ha encontrado una alta proporción de óxido de limoneno y piperitenona (ausente en F. vulgare) en la composición de aceite esencial de los frutos secos de F. sanguineum y una elevada cantidad (aproximadamente 50%) de α-felandreno en sus raíces y tallos. El análisis filogenético se realizó utilizando las secuencias del espaciador transcrito interno de ADN ribosomal nuclear (ITS) y las secuencias del gen cloroplástico rbcL. El análisis ITS apoya la existencia de la nueva especie, al tiempo que revela la divergencia de secuencias tanto a nivel intraespecífico como a nivel interespecífico. La divergencia de secuencia encontrada en el gen cloroplástico, aunque reducida a un nucleótido, proporcionó apoyo adicional para la caracterización de la nueva especie, para la que se propone el nombre de Foeniculum sanguineum.

Molecular Identification of Fitzroya Cupressoides, Sequoia Sempervirens, and Thuja Plicata Wood Using Taxon-Specific RDNA-ITS Primers

IAWA Journal ◽  
2011 ◽  
Vol 32 (2) ◽  
pp. 273-284 ◽  
Author(s):  
Felix Hanssen ◽  
Niko Wischnewski ◽  
Ute Moreth ◽  
Elisabeth A. Magel
Keyword(s):  
Sequence Divergence ◽  
Its Region ◽  
Sequoia Sempervirens ◽  
Nuclear Ribosomal Dna ◽  
Thuja Plicata ◽  
Length Variation ◽  
Rdna Its ◽  
Its Regions ◽  
Rdna Its Region ◽  
Fitzroya Cupressoides

The nuclear ribosomal DNA internal transcribed spacer (rDNA-ITS) region was PCR amplified and sequenced from the wood of three specimens of Fitzroya cupressoides, nine specimens of Sequoia sempervirens, and ten specimens of Thuja plicata. The full lengths of the ITS regions are 1110 bp for F. cupressoides, 1096 bp for S. sempervirens, and 1138 bp for T. plicata, and thus in the range of 975 bp to 1125 bp which is reported for members of the Cupressaceae. Length variation of ITS regions is due to differences in the length of the spacer region ITS1. Intraspecific variations of the sequences of rDNA-ITS regions were one bp in F. cupressoides, and 18 bp in S. sempervirens and T. plicata. Based on the interspecific sequence divergence of the ITS region, taxon-specific primers were designedfor the detection of F. cupressoides, S. sempervirens and T. plicata. The primer sequences were selected from the highly divergent ITS1 spacer. The specificity of the primers was checked by lengths and sequence of the amplicons, and the primers detected the target organism, solely, across 40 conifer species. Our data establish the molecular basis for DNA-based wood identification in these species.

BRAZILIAN SPECIES OF VIGUIERA (ASTERACEAE) EXHIBIT LOW LEVELS OF ITS SEQUENCE VARIATION

2000 ◽  
Vol 57 (3) ◽  
pp. 323-332 ◽  
Author(s):  
E. E. SCHILLING ◽  
F. B. DA COSTA ◽  
N. P. LOPES ◽  
P. J. HEISE
Keyword(s):  
Sequence Variation ◽  
Its Region ◽  
Taxonomic Diversity ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
South American ◽  
Low Level ◽  
Chemical Variability ◽  
Recent Addition ◽  
Striking Contrast

The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA was sequenced from 21 accessions of Viguiera from South America, including 14 from Brazil. Overall there was only a small amount of sequence variation, less than 3.4% among South American samples and less than 4.5% between the South American samples and the Mexican V. flava. Phylogenetic analysis revealed little divergence among the Brazilian samples of Viguiera. The low level of ITS sequence variation was in striking contrast to the taxonomic diversity and chemical variability that have been reported for Viguiera in Brazil. The low level of sequence variation suggests that, despite its clear morphological and phytochemical adaptations to the cerrado, Viguiera is probably a relatively recent addition (less than 3 million years) to the flora of this area.

Differentiation of Hemicriconemoides mangiferae and H. litchi (Nematoda: Criconematina) based on morphometrics and nuclear ribosomal DNA sequences

Nematology ◽  
2011 ◽  
Vol 13 (2) ◽  
pp. 165-175 ◽  
Author(s):  
Ruey-Shyang Chen ◽  
Hui-Fang Ni ◽  
Tung-Tsuan Tsay ◽  
Diann-Yih Chen
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Its Region ◽  
Rdna Sequence ◽  
Nuclear Ribosomal Dna ◽  
Molecular Characteristics ◽  
Species Differentiation ◽  
Sequence Information ◽  
Lateral Field

Abstract Hemicriconemoides mangiferae and H. litchi, which have been considered as junior synonyms of H. strictathecatus, are morphologically similar, making identification difficult. In the present study, six populations of Hemicriconemoides spp. were collected from mango and litchi in Taiwan and were differentiated based on morphometrics and molecular characteristics. By comparing morphometric data from females and males, three populations collected from mango were identified as H. mangiferae and another three populations from litchi were identified as H. litchi. According to SEM, both of the H. mangiferae and H. litchi males had an areolated lateral field with four incisures; caudal alae were not found. The internal transcribed spacer (ITS) sequences of ribosomal DNA (rDNA) from these nematode populations were sequenced and aligned. The sequence identity of the ITS region was 89-95% between H. mangiferae and H. litchi populations, suggesting rDNA sequence divergence could be a taxonomic aid for species differentiation. Since H. mangiferae and H. litchi are closely related to H. strictathecatus, more rDNA sequence information could be valuable to deal with molecular phylogenetic relationships of these species in depth.

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