FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa

Joachimiak, Andrzej J.; Hasterok, Robert; Śliwińska, Elwira; Musiał, Krystyna; Grabowska-Joachimiak, Aleksandra

doi:10.1007/s00709-018-1238-9

Cited by 11 publications

(4 citation statements)

References 53 publications

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“…Although introgression and hybridization is also relatively frequent in the banana genus (Němečková et al, 2018) a more likely explanation for complex graph structures in Musa acuminata ( Figure 6C) is an exceptionally high number of 5S rDNA loci in this species (six per diploid genome) (Valarik et al, 2002;Garcia et al, 2012a) and probably inefficient interlocus recombination ( Schlotterer and Tau tz,19 94) lea ding to poor homogenization. Actually, the mechanisms of amplification of 5S rDNA loci across the chromosomes are still poorly understood (Schubert and Wobus, 1985;Symonova et al, 2017;Joachimiak et al, 2018;Souza et al, 2019). 3.…”

Section: Evaluation Of the Graph-based Methods For Identification Of Amentioning

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: Evaluation Of the Graph-based Methods For Identification Of Amentioning

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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“…Both these sections (diploids and tetraploids) differ in their nuclear 2C DNA contents (ca. 11 pg vs. 21-22 pg, respectively) (Joachimiak et al, 2018).…”

Section: The Study Taxonmentioning

confidence: 93%

“…Excessive accumulation of 5S rDNA clusters in Aconitum chromosomes (FISH) in the tetraploid species (A. firmum and A. plicatum), followed by a reduction of the basal genome size (Joachimiak et al, 2018), likely occurred during diploidization, which is one of the stages of the cyclical process described as the "wondrous cycle of polyploidy" in plants. It could be a nonrandom process, as suggested by the retention of the original diploid ancestral progenitor genomes (Wendel, 2015), at least partially responsible for the paraphyly of the tetraploid and polyphyly of the diploid clades.…”

Section: Independent Evolution Of Diploid and Tetraploid Linesmentioning

confidence: 99%

Phylogeny of Aconitum Subgenus Aconitum in Europe

et al. 2020

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Phylogenetic relations within Aconitum subgen. Aconitum (Ranunculaceae) in Europe are still unclear. To infer the phylogeny of the nuclear (ITS) region and chloroplast intergenic spacer trnL(UAG)-ndhF of the chloroplast DNA (cpDNA), we analyzed 64 accessions within this taxon, 58 from Europe and six from the Caucasus Mts. Nuclear ITS sequences were identical in 51 European and two Caucasian accessions, whereas the remaining sequences were unique. cpDNA sequences could be categorized into five haplotypes, i.e., A–E, including a European-Caucasian Aconitum haplotype B. Ten cpDNA sequences were unique. A 5-bp indel distinguished the diploids from the tetraploids. None of the extant European diploids were basal to the tetraploid local group. A phylogenetic tree based on combined ITS and cpDNA sequences (bayesian inference, maximum likelihood, minimal parsimony) placed Aconitum burnatii (Maritime Alps, Massif Central) and A. nevadense (Sierra Nevada, Pyrenees) in a sister group to all other European species. A Bayesian relaxed clock model estimated the earliest split of the Caucasian species during the Late Miocene [ca. 7 million years ago (Mya)], and the divergence of A. burnatii and A. nevadense from the European genetic stock during the Miocene/Pliocene (ca. 4.4 Mya). Diploids in Europe are likely to be descendants of the Miocene European-Caucasian flora linked with the ancient Asian (arctiotertiary) genetic stock. The origins of the tetraploids remain unclear, and it is possible that some tetraploids originated from local, now extinct diploids. Both the diploids and tetraploids underwent rapid differentiation in the Late Pliocene – Quaternary period.

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“…exhibit bimodal karyotypes, meaning they have two sets of chromosomes of contrasting sizes (Joachimiak et al, 2018;Baéz et al, 2019). Most of these plants have eight chromosomes, two of which are large and submetacentric, whereas six are small and primarily submetacentric (Joachimiak et al, 2018) (Figure 4). However, A. fletcheranum is the only Aconitum sp.…”

Section: Diversity At Ploidy Level Inmentioning

confidence: 99%

The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum

Kakkar,

Haneen,

Parida

et al. 2023

Front. Plant Sci.

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Humanity will always be indebted to plants. In the ongoing scientific era, the ‘Herbal Revolution’ has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.

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FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa

Cited by 11 publications

References 53 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

Phylogeny of Aconitum Subgenus Aconitum in Europe

The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum

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