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

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.

Download Full-text

Multiple Hybrid Formation in Natural Populations: Concerted Evolution of the Internal Transcribed Spacer of Nuclear Ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae)

Molecular Biology and Evolution ◽

10.1093/molbev/msg046 ◽

2003 ◽

Vol 20 (3) ◽

pp. 338-350 ◽

Cited By ~ 154

Author(s):

M. A. Koch

Keyword(s):

Ribosomal Dna ◽

North American ◽

Concerted Evolution ◽

Internal Transcribed Spacer ◽

Natural Populations ◽

Nuclear Ribosomal Dna ◽

Hybrid Formation

Download Full-text

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

Genome ◽

10.1139/g97-796 ◽

1997 ◽

Vol 40 (5) ◽

pp. 730-743 ◽

Cited By ~ 49

Author(s):

Malika L. Ainouche ◽

Randall J. Bayer

Keyword(s):

Ribosomal Dna ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Direct Sequencing ◽

Diploid Species ◽

Pcr Amplification ◽

Nuclear Ribosomal Dna ◽

Species Introduction ◽

Bromus Hordeaceus ◽

Allotetraploid Species

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.

Download Full-text

The Evolution of Ribosomal DNA Divergent Paralogues and Phylogenetic Implications

Genetics ◽

10.1093/genetics/145.3.821 ◽

1997 ◽

Vol 145 (3) ◽

pp. 821-832 ◽

Cited By ~ 8

Author(s):

Edward S Buckler ◽

Anthony Ippolito ◽

Timothy P Holtsford

Keyword(s):

Secondary Structure ◽

Ribosomal Dna ◽

Concerted Evolution ◽

Internal Transcribed Spacer ◽

High Stability ◽

Nuclear Ribosomal Dna ◽

Structure Stability ◽

Phylogenetic Implications ◽

Ancestral States ◽

Pcr Conditions

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serveas good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.

Download Full-text

Intra-genomic variability and pseudogenes in ribosomal ITS regions of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae)

Animal Biology ◽

10.1163/15707563-20191141 ◽

2020 ◽

Vol 70 (2) ◽

pp. 145-158 ◽

Cited By ~ 1

Author(s):

Li Gong ◽

Xiaoyu Kong ◽

Hairong Luo ◽

Shixi Chen ◽

Wei Shi ◽

...

Keyword(s):

Internal Transcribed Spacer ◽

Minimum Free Energy ◽

Sequence Type ◽

Nuclear Ribosomal Dna ◽

Sequence Length ◽

Type B ◽

Genomic Variability ◽

Future Studies ◽

Rdna Sequences ◽

Its Regions

Abstract Eukaryotic nuclear ribosomal DNA (rDNA) typically evolves in a concerted manner, in which hundreds of rDNA sequences within species show little or no variations, whereas the sequences of different species diverge. There are few studies of the internal transcribed spacer regions (ITS1-5.8S-ITS2) in teleostean fishes and only one report on flatfishes. Here, we reported the discovery of two types of highly divergent ITS1-5.8S-ITS2 rDNA sequences (Type A and B) in the genome of the Bloch’s tonguesole, Paraplagusia blochii. These sequences mainly differ in sequence length, secondary structure, and minimum free energy. According to the potential features of pseudogenes, Type B sequences are speculated to be putative pseudogenic ITS regions. Cluster analyses also supported two major clades that corresponded to the sequence type. To the best of our knowledge, this is the first report of the ITS regions of tonguefish, and may therefore provide useful information for future studies of the rDNA of flatfishes as well as the patterns of rDNA evolution in teleostean fishes.

Download Full-text

Genetic diversity and molecular evolution of the internal transcribed spacer (ITSs) of nuclear ribosomal DNA in the Tunisian fig cultivars (Ficus carica L.; Moracea)

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2012.11.017 ◽

2013 ◽

Vol 48 ◽

pp. 20-33 ◽

Cited By ~ 9

Author(s):

Baraket Ghada ◽

Ben Abdelkrim Ahmed ◽

Mars Messaoud ◽

Salhi-Hannachi Amel

Keyword(s):

Genetic Diversity ◽

Molecular Evolution ◽

Ribosomal Dna ◽

Internal Transcribed Spacer ◽

Ficus Carica ◽

Nuclear Ribosomal Dna

Download Full-text

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.92.15.6813 ◽

1995 ◽

Vol 92 (15) ◽

pp. 6813-6817 ◽

Cited By ~ 370

Author(s):

T. Sang ◽

D. J. Crawford ◽

T. F. Stuessy

Keyword(s):

Ribosomal Dna ◽

Concerted Evolution ◽

Internal Transcribed Spacer ◽

Reticulate Evolution ◽

Nuclear Ribosomal Dna ◽

Internal Transcribed Spacer Sequences

Download Full-text

Molecular Evolution and Phylogenetic Implications of Internal Transcribed Spacer Sequences of Nuclear Ribosomal DNA in the Phaseolus–Vigna Complex

Molecular Phylogenetics and Evolution ◽

10.1006/mpev.2001.1037 ◽

2002 ◽

Vol 22 (1) ◽

pp. 1-19 ◽

Cited By ~ 46

Author(s):

S Goel ◽

S.N Raina ◽

Y Ogihara

Keyword(s):

Molecular Evolution ◽

Ribosomal Dna ◽

Internal Transcribed Spacer ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Implications ◽

Internal Transcribed Spacer Sequences

Download Full-text

Exploring Evolutionary Dynamics of nrDNA in Carex Subgenus Vignea (Cyperaceae)

Systematic Botany ◽

10.1600/036364408785679860 ◽

2008 ◽

Vol 33 (3) ◽

pp. 514-524 ◽

Cited By ~ 16

Author(s):

Matthew G. King ◽

Eric H. Roalson

Keyword(s):

Concerted Evolution ◽

Evolutionary Dynamics ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Ribosomal Subunit ◽

Nuclear Ribosomal Dna ◽

Phylogeny Reconstruction ◽

Lineage Sorting ◽

Future Studies ◽

Carex Subgenus Vignea

Nuclear ribosomal DNA (nrDNA) has been used for more than a decade in species level phylogenetic analyses. While nrDNA can often be a powerful phylogenetic marker, intraindividual polymorphisms of the internal and external transcribed spacers (ITS, ETS) can lead to problems in their use for phylogeny reconstruction. Incomplete concerted evolution coupled with hybridization and incomplete lineage sorting can further exacerbate these problems. Previous phylogenetic analyses using nrDNA of Carex subgenus Vignea suggest that the current sectional classifications may be highly artificial. We endeavored to identify what influence incomplete concerted evolution, lineage sorting, and hybridization have played in the complex patterns of relationships previously inferred from ITS and ETS sequences for subgenus Vignea. Through comprehensive cloning we identified high levels of intraindividual polymorphisms and in many cases this led to the polyphyly of individuals. Furthermore, individuals identified with novel mutations in the 5.8S ribosomal subunit did not show a significant deviation in G-C percentage and free energy. Based on these results we suggest that nrDNA contains multiple paralogs in many species and clades within Carex subgenus Vignea which greatly complicates its use for phylogenetic inference of relationships and future studies in Carex need to take this into account.

Download Full-text