Concerted evolution rapidly eliminates sequence variation in rDNA coding regions but not in intergenic spacers in Nicotiana tabacum allotetraploid

Lunerová, Jana; Renny‐Byfield, Simon; Matyášek, Roman; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.1007/s00606-017-1442-7

Cited by 25 publications

(23 citation statements)

References 74 publications

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“…A strong repeat-rich locus likely occurs in the S. maritima parent while a weaker locus may be present in the S. alterniflora parent. These examples demonstrate a higher sensitivity of a cluster graph-based approach over the de novo assembly or PCR-cloning approaches, where various technical biases may occur (Lunerova et al, 2017).…”

Section: Dynamism Of Rdna Loci In Hybrid Genomesmentioning

confidence: 99%

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

et al. 2020

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Introduction: Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.Results: (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. Conclusion:We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.

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Section: Dynamism Of Rdna Loci In Hybrid Genomesmentioning

confidence: 99%

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

et al. 2020

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“…ITS is often used to infer the relationships based on nuclear sequences in plants and can also help ascertain the parents of polyploids (Alvarez and Wendel, ). However, concerted evolution may result in the retention of only one parental copy (Wendel et al., ; Lunerová et al., ). Here, we suggest evolutionary hypotheses regarding the origins and relationships of the ploidal levels in Lippia alba based on nuclear and plastid genes, SSRs, and morphological and chemical data.…”

Section: Discussionmentioning

confidence: 99%

Genetic relationships and polyploid origins in the Lippia alba complex

Lopes

Carvalho

Zorzatto

et al. 2020

American J of Botany

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Premise Plant genomes vary in size and complexity due in part to polyploidization. Latitudinal analyses of polyploidy are biased toward floras of temperate regions, with much less research done in the tropics. Lippia alba has been described as a tropical polyploid complex with diploid, triploid, tetraploid, and hexaploid accessions. However, no data regarding relationships among the ploidal levels and their origins have been reported. Our goals are to clarify the relationships among accessions of Lippia alba and the origins of each ploidal level. Methods We investigated 98 samples representing all five geographical regions of Brazil and all ploidal levels using microsatellite (SSR) allelic variation and DNA sequences of ITS and trnL‐F. Nine morphological structures were analyzed from 33 herbarium samples, and the chemical compounds of 78 accessions were analyzed by GC–MS. Results Genetic distance analysis, the alignment block pattern, as well as RAxML and Bayesian trees showed that accessions grouped by ploidal level. The triploids form a well‐defined group that originated from a single group of diploids. The tetraploids and hexaploid grouped together in SSR and trnL‐F analyses. The recovered groups agree with chemical data and morphology. Conclusions The accessions grouped by ploidal level. Only one origin of triploids from a single group of diploids was observed. The tetraploid origin is uncertain; however, it appears to have contributed to the origin of the hexaploid. This framework reveals linkages among the ploidal levels, providing new insights into the evolution of a polyploid complex of tropical plants.

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“…By contrast, if the tetraploids were allopolyploids, we could expect genetic admixture in the AFLP analyses, the presence of divergent DET1 sequences (pointing to homeologous loci) placed in distinct phylogenetic clades together with the respective diploids and additivity of genome size values (e.g., Jakob and Blattner, ; Brassac et al., ; Díaz‐Pérez et al., ; Mandák et al., ; Padilla‐García et al., ). The ITS region, because of concerted evolution, which can operate to various extents and in different directions, may display a variety of patterns after hybridization (reviewed by Álvarez and Wendel, ; Nieto Feliner and Rosselló, 2014a, see examples e.g., in Zozomová‐Lihová et al., 2014a; Krak et al., ; Lunerová et al., ).…”

Section: Discussionmentioning

confidence: 99%

Diversification and independent polyploid origins in the disjunct species Alyssum repens from the Southeastern Alps and the Carpathians

Melichárková

Španiel

Marhold

et al. 2019

American J of Botany

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Premise Disjunct distributions have been commonly observed in mountain plant species and have stimulated phylogeographic and phylogenetic research. Here we studied Alyssum repens, a member of the polyploid species complex A. montanum−A. repens, which exhibits SE Alpine‐Carpathian disjunctions with a large elevational span and consists of diploid and tetraploid populations. We aimed to investigate the species‘ genetic and cytotype structure in the context of its distribution patterns, to elucidate the polyploid origins and to propose an appropriate taxonomic treatment. Methods We combined AFLP fingerprinting markers, sequence variation of the highly repetitive ITS region of rDNA and the low‐copy DET1 nuclear gene, genome size, and morphometric data. Results We identified four geographically structured genetic lineages. One consisted of diploid populations from the foothills of the Southeastern Alps and neighboring regions, and the three others were allopatric montane to alpine groups comprising diploids and tetraploids growing in the Southeastern Carpathians and the Apuseni Mts. in Romania. Conclusions We inferred a vicariance scenario associated with Quaternary climatic oscillations, accompanied by one auto‐ and two allopolyploidization events most likely involving a northern Balkan relative. Whereas genetic differentiation and allopatric distribution would favor the taxonomic splitting of this species, the genetic lineages largely lack morphological distinguishability, and their ecological, cytotype and genome size divergence is only partial. Even though we probably face here a case of incipient speciation, we propose to maintain the current taxonomic treatment of Alyssum repens as a single, albeit variable, species.

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Concerted evolution rapidly eliminates sequence variation in rDNA coding regions but not in intergenic spacers in Nicotiana tabacum allotetraploid

Cited by 25 publications

References 74 publications

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

Genetic relationships and polyploid origins in the Lippia alba complex

Diversification and independent polyploid origins in the disjunct species Alyssum repens from the Southeastern Alps and the Carpathians

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