On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid–diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli–henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli–henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the tetraploid Bromus adoensis are sister taxa within section Bromus; they belong in a weakly differentiated clade with the diploids Bromus brachystachys, Bromus japonicus, Bromus squarrosus, Bromus arvensis, and Bromus intermedius.Key words: Bromus, allopolyploidy, ITS, ribosomal DNA, phylogeny.

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Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽

10.1139/g95-026 ◽

1995 ◽

Vol 38 (2) ◽

pp. 211-223 ◽

Cited By ~ 147

Author(s):

C. Hsiao ◽

N. J. Chatterton ◽

K. H. Asay ◽

K. B. Jensen

Keyword(s):

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Parallel Evolution ◽

Diploid Species ◽

Its Region ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

The Arctic ◽

Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

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(269) Taxonomic Relationship of Korean Native Aster, Based on Internal Transcribed Spacer (ITS) Sequences of Nuclear Ribosomal DNA

HortScience ◽

10.21273/hortsci.40.4.1017a ◽

2005 ◽

Vol 40 (4) ◽

pp. 1017A-1017

Author(s):

Su-Young Hong ◽

Kwang-Soo Cho ◽

Ki-Oug Yoo ◽

Jong-Taek Suh ◽

Dong-Lim Yoo

Keyword(s):

Ribosomal Dna ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Its Region ◽

Sister Group ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Position ◽

Its2 Region ◽

Base Pairs ◽

Total Length

There are 25 species of aster in Korea. There is a controversy about the taxonomical classification of Aster. The genus Aster was classified into four genera, Aster, Gymnaster, Kalimeris, and Heteropappus, by morphological characters. In order to clarify the phylogenetic position of aster, the nucleotide sequence of the nuclear ribosomal DNA internal transcribed spacer (ITS) region was compared among 11 taxa in Korean native aster. The size of ITS1 and ITS2 ranged from 283 to 286 bp and from 251 to 257 bp, respectively. The size of 5.8S region was 164 bp in 11 taxa. The total length of ITS1, 5.8S and ITS2, A. tripolium was shown to be the shortest length, 701 bp; and A. scaber was shown to be the longest length, 706 bp. The G+C content of ITS1 ranged from 47.9% to 51.2% and ITS2 ranged from 52.2% to 55.1%. The range of each taxon was narrow. The total length of the character matrix was 708 characters. Among them, total indel showed 9; in the ITS1 region indel showed 6 it was 67%; and in the ITS2 region, indel showed 3. Most of the indels showed deletion or insertion of only one base pair, but in A. spathulifolius deleted two base pairs and in A. tripolium deleted five base pairs. But in A. yomena, A. hayatae, A. koraiensis, and A. hispidus, the indel was not detected. Phylogenetic trees did not even make a difference inter-genus, but A. yomena and A. koraiensis called genus Kalimeris and genus Gymnaster, respectively; these constituted a clade. A. hispidus called genus Heteropappus was placed as a sister group to the clade of A. ageratoides and A. glehni.

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A molecular perspective on the genera Paragonimus Braun, Euparagonimus Chen and Pagumogonimus Chen

Journal of Helminthology ◽

10.1017/s0022149x99000499 ◽

1999 ◽

Vol 73 (4) ◽

pp. 295-299 ◽

Cited By ~ 33

Author(s):

D. Blair ◽

B. Wu ◽

Z.S. Chang ◽

X. Gong ◽

T. Agatsuma ◽

...

Keyword(s):

Ribosomal Dna ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Morphological Study ◽

Type Species ◽

Phylogenetic Trees ◽

Nuclear Ribosomal Dna ◽

Mitochondrial Cytochrome ◽

The Status ◽

Second Internal Transcribed Spacer

The status of the genera Euparagonimus Chen, 1963 and Pagumogonimus Chen, 1963 relative to Paragonimus Braun, 1899 was investigated using DNA sequences from the mitochondrial cytochrome c oxidase subunit I (CO1) gene (partial) and the nuclear ribosomal DNA second internal transcribed spacer (ITS2). In the phylogenetic trees constructed, the genus Pagumogonimus is clearly not monophyletic and therefore not a natural taxon. Indeed, the type species of Pagumogonimus,P. skrjabini from China, is very closely related to Paragonimusmiyazakii from Japan. The status of Euparagonimus is less obvious. Euparagonimus cenocopiosus lies distant from other lungflukes included in the analysis. It can be placed as sister to Paragonimus in some analyses and falls within the genus in others. A recently published morphological study placed E. cenocopiosus within the genus Paragonimus and probably this is where it should remain.

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Multiple Origins and nrDNA Internal Transcribed Spacer Homeologue Evolution in the Glycine tomentella (Leguminosae) Allopolyploid Complex

Genetics ◽

10.1093/genetics/166.2.987 ◽

2004 ◽

Vol 166 (2) ◽

pp. 987-998 ◽

Cited By ~ 1

Author(s):

Jason T Rauscher ◽

Jeff J Doyle ◽

A H D Brown

Keyword(s):

Molecular Evolution ◽

Concerted Evolution ◽

Internal Transcribed Spacer ◽

Direct Sequencing ◽

Nuclear Ribosomal Dna ◽

Nucleolar Dominance ◽

Future Studies ◽

Complex Interactions ◽

Multiple Origins ◽

Glycine Tomentella

Abstract Despite the importance of polyploidy in the evolution of plants, patterns of molecular evolution and genomic interactions following polyploidy are not well understood. Nuclear ribosomal DNA is particularly complex with respect to these genomic interactions. The composition of nrDNA tandem arrays is influenced by intra- and interlocus concerted evolution and their expression is characterized by patterns such as nucleolar dominance. To understand these complex interactions it is important to study them in diverse natural polyploid systems. In this study we use direct sequencing to isolate and characterize nrDNA internal transcribed spacer (ITS) homeologues from multiple accessions of six different races in the Glycine tomentella allopolyploid complex. The results indicate that in most allopolyploid accessions both homeologous nrDNA repeats are present, but that there are significant biases in copy number toward one homeologue, possibly resulting from interlocus concerted evolution. The predominant homeologue often differs between races and between accessions within a race. A phylogenetic analysis of ITS sequences provides evidence for multiple origins in several of the polyploid races. This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression.

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