rDNA Loci Evolution in the Genus Glechoma (Lamiaceae)

Jang, Tae‐Soo; McCann, Jamie; Parker, John; Takayama, Kōji; Hong, Suk‐Pyo; Schneeweiss, Gerald M.; Weiss‐Schneeweiss, Hanna

doi:10.1371/journal.pone.0167177

Cited by 24 publications

(13 citation statements)

References 54 publications

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“…The difference in base chromosome number between Chinese-Korean (x = 11) and Japanese (x = 10) populations strongly indicated that the Korean populations of C. japonicum are more closely related to Chinese populations compared to the Japanese populations based on base chromosome numbers, and this result was consistent with population genetic analyses using ISSR and SCoT markers [5,6]. Thus, further studies, including physical mapping of chromosomes using FISH (fluorescence in situ hybridization) as well as molecular phylogenomics and population genomics of C. japonicum and its closely related species, could help clarify the evolutionary history of C. japonicum [19,[34][35][36][37][38][39][40].…”

Section: Resultssupporting

confidence: 79%

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Choi

Gang²,

Kim

et al. 2021

Plants

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Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady’s slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady’s slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady’s slipper orchid species.

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Section: Resultssupporting

confidence: 79%

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Choi

Gang²,

Kim

et al. 2021

Plants

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“…This phenomenon has been reported in many different plant genera including Brassica and Paphiopedilum (Hasterok et al 2006 ; Lan and Albert 2011 ). Similar to many other species, the FISH patterns of the 35S rDNA sites in the Allium species were more polymorphic than those of the 5S rDNA (Chiarini et al 2017 ; Garcia et al 2017 ; Jang et al 2016 ). In addition, an intraspecific polymorphism was observed in the 5S rDNA sites number in A .…”

Section: Discussionmentioning

confidence: 85%

Karyotype analysis of eight cultivated Allium species

et al. 2018

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The karyotypes of Allium , a genus that comprises many crops and ornamental plants, are relatively poorly studied. To extend our knowledge on karyotype structure of the genus, the chromosomal organization of rRNA genes and CMA/DAPI bands was studied. Fluorescence in situ hybridization using 5S and 35S rDNA probes and banding methods (silver staining and CMA 3 /DAPI staining) were used to analyze the karyotypes of eight cultivated Allium L. species. Analyzed Allium taxa revealed three different basic chromosome numbers ( x = 7, 8, 9) and three different ploidy levels (diploid, triploid, and tetraploid). The rDNA sites chromosomal organization is reported the first time for the six species ( A . moly , A . oreophilum , A . karataviense , A . nigrum , A . sphaerocephalon , A . porrum ). The Allium species that were analyzed showed a high level of interspecies polymorphism in the number and localization of the rDNA sites. The fluorescence in situ hybridization patterns of 35S rDNA sites were more polymorphic than those of the 5S rDNA in the diploid species. Several groups of similar chromosomes could be distinguished among the chromosomes that had rDNA sites in the polyploid species. Each of the groups had three chromosomes (triploid A . sphaerocephalon L.) or four chromosomes (tetraploid A . porrum L.) suggesting their autopolyploid origin. In the genomes of four of the analyzed species, only some of the 35S rDNA sites were transcriptionally active. Fluorochrome banding revealed that the CMA 3 + bands were associated with the 35S rDNA sites in all of the species that were analyzed, except A . fistulosum L. in which positive CMA 3 + bands were detected in the terminal position of all of the chromosome arms. The rDNA sequences, nucleolar organizer regions (NORs), and CMA/DAPI bands are very good chromosome markers that allowed to distinguished from two to five pairs of homologous chromosomes in analyzed Allium species. The karyotypes of the studied species could be clearly distinguished by the number and position of the rDNA sites, NORs, and CMA/DAPI bands, which revealed high interspecific differentiation among the taxa. Electronic supplementary material The online version of this article (10.1007/s13353-018-0474-1) contains supplementary material, which is available to authorized users.

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“…Most studies have used classical single clone sequencing approaches whereas high-throughput data have only rarely been employed and are limited to the 35S (45S) rDNA (Matyasek et al, 2012;West et al, 2014;Boutte et al, 2016). The analysis of 5S rDNA is also informative and has been successfully used in many phylogenetic studies (Cronn et al, 1996;Fulnecek et al, 2002;Baum et al, 2004;Besendorfer et al, 2005;Volkov et al, 2007;Baum et al, 2012;Jang et al, 2016). Its analysis is complementary to that of 35S since both loci usually occur separately on chromosomes (Roa and Guerra, 2012;Garcia et al, 2017).…”

Section: Discussionmentioning

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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rDNA Loci Evolution in the Genus Glechoma (Lamiaceae)

Cited by 24 publications

References 54 publications

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Karyotype analysis of eight cultivated Allium species

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

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