Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes

Vitales, Daniel; D'Ambrosio, Ugo; Gálvez, Francisco; Kovařı́k, Aleš; Garcia, Sònia

doi:10.1007/s00606-017-1440-9

Cited by 29 publications

(21 citation statements)

References 40 publications

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“…Despite all the telomere motif exceptions detected, the real diversity in telomeric sequences in land plants is probably greatly underestimated. A recent publication (Vitales et al, 2017), in which a screening of land plant telomere sequences was performed, found that telomere sequences were only known clearly for less than 10% of the species and 40% of the genera contained in the Plant rDNA database (www.plantrdnadatabase. com), a resource providing molecular cytogenetics information on land plants (Garcia et al, 2012).…”

Section: How Variable Are Telomere Sequences?mentioning

confidence: 99%

Origin, Diversity, and Evolution of Telomere Sequences in Plants

Peška

Garcia

2020

Front. Plant Sci.

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Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (T x A y G z) n. Although they are well conserved across large groups of organisms, recent findings in plants imply that their diversity has been underestimated. Changes in telomeres are of enormous evolutionary importance as they can affect whole-genome stability. Even a small change in the telomere motif of each repeat unit represents an important interference in the system of sequence-specific telomere binding proteins. Here, we provide an overview of telomere sequences, considering the latest phylogenomic evolutionary framework of plants in the broad sense (Archaeplastida), in which new telomeric sequences have recently been found in diverse and economically important families such as Solanaceae and Amaryllidaceae. In the family Lentibulariaceae and in many groups of green algae, deviations from the typical plant telomeric sequence have also been detected recently. Ancestry and possible homoplasy in telomeric motifs, as well as extant gaps in knowledge are discussed. With the increasing availability of genomic approaches, it is likely that more telomeric diversity will be uncovered in the future. We also discuss basic methods used for telomere identification and we explain the implications of the recent discovery of plant telomerase RNA on further research about the role of telomerase in eukaryogenesis or on the molecular causes and consequences of telomere variability.

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Section: How Variable Are Telomere Sequences?mentioning

confidence: 99%

Origin, Diversity, and Evolution of Telomere Sequences in Plants

Peška

Garcia

2020

Front. Plant Sci.

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“…Molecular cytogenetic mapping of the nuclear ribosomal RNA genes encoding for 35S (18S-5.8S-25S) and 5S rDNAs have proved useful for identifying the patterns and dynamics of chromosomal changes in closely related species groups (Jang et al, 2013(Jang et al, , 2016aVitales et al, 2017). The distribution of rDNA loci has been reported for some Korean monocots, as summarized in Table 1 (data retrieved from Plant rDNA Database; http:// www.plantrdnadatabase.com/, 2018 May 22).…”

Section: Patterns Of Genome Evolution: the Use Of Molecular Cytogenetmentioning

confidence: 99%

“…The chromosome numbers in Korean non-Commelinids monocots have previously been reported for a number of taxonomically closely related taxa (Rice et al, 2015, references therein), although the incidence of polyploids and its evolutionary aspects have not been addressed in detail. It is therefore timely to summarize the knowledge of chromosome numbers, genome sizes, and polyploidy incidence in the Korean monocots (Rice et al, 2015;Vitales et al, 2017) and to identify the most important taxonomic groups in which questions of chromosomal evolution can be addressed most effectively.…”

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confidence: 99%

“…The genome size values and ploidy level inferences in Korean non-Commelinids monocots were retrieved from the Plant DNA C-values database (http://www.kew.org/cvalues/, accessed on 2018 May 22) (Bennett and Leitch, 2012). The data on number and chromosomal localization of rDNA loci (5S and 35S rDNA) in Korean non-Commelinids monocots obtained applying fluorescent in situ hybridization were retrieved from the third release of the plant rDNA database (Vitales et al, 2017;http://www.plantrdnadatabase.com/, accessed on 2018 May 22).…”

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Chromosome numbers and polyploidy events in Korean non-commelinids monocots: A contribution to plant systematics

Jang

Weiss‐Schneeweiss

2018

Korean J. Pl. Taxon

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The evolution of chromosome numbers and the karyotype structure is a prominent feature of plant genomes contributing to or at least accompanying plant diversification and eventually leading to speciation. Polyploidy, the multiplication of whole chromosome sets, is widespread and ploidy-level variation is frequent at all taxonomic levels, including species and populations, in angiosperms. Analyses of chromosome numbers and ploidy levels of 252 taxa of Korean non-commelinid monocots indicated that diploids (ca. 44%) and tetraploids (ca. 14%) prevail, with fewer triploids (ca. 6%), pentaploids (ca. 2%), and hexaploids (ca. 4%) being found. The range of genome sizes of the analyzed taxa (0.3-44.5 pg/1C) falls well within that reported in the Plant DNA C-values database (0.061-152.33 pg/1C). Analyses of karyotype features in angiosperm often involve, in addition to chromosome numbers and genome sizes, mapping of selected repetitive DNAs in chromosomes. All of these data when interpreted in a phylogenetic context allow for the addressing of evolutionary questions concerning the large-scale evolution of the genomes as well as the evolution of individual repeat types, especially ribosomal DNAs (5S and 35S rDNAs), and other tandem and dispersed repeats that can be identified in any plant genome at a relatively low cost using next-generation sequencing technologies. The present work investigates chromosome numbers (n or 2n), base chromosome numbers (x), ploidy levels, rDNA loci numbers, and genome size data to gain insight into the incidence, evolution and significance of polyploidy in Korean monocots.

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“…5S rDNA contains a highly conserved coding region of 120 bp and a non-transcribed spacer (NTS region that varies between 100 and 900 bp). As relatively stable and reliable molecular cytogenetic markers, the characteristics of 45S and 5S rDNA on chromosomes provide useful information for chromosome research [27][28][29]. The FISH positions of rDNAs on chromosomes directly provide an effective method for chromosome identi cation and the research of chromosome organization and evolution.…”

Section: Introductionmentioning

confidence: 99%

Comparative chromosomal localization of 45S and 5S rDNAs in 76 purple-fleshed sweet potato cultivars

Chen

Sun

et al. 2020

Preprint

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Background: In recent years, purple-fleshed sweet potato has been paid more and more attention because of its high nutritional value. However, the current studies on purple-fleshed sweet potato were still focused on the research and production of the related products. The research on its cytogenetics is relatively lagging behind, which cannot satisfy the study of genetic diversity of purple-fleshed sweet potato. Therefore, we carried out cytogenetic analysis on 76 purple-fleshed sweet potato cultivars, aim to analyze the chromosome structure and distribution of 45S rDNA and 5S rDNA in 76 purple-fleshed sweet potato cultivars.Results: We have found that only 62 purple-fleshed sweet potato cultivars with 90 chromosomes, and the others were aneuploid with 88, 89, 91, 92 chromosomes. The number of 45S rDNA in 76 purple-fleshed sweet potato cultivars varies from 16 to 21, with different signal sizes and intendities, and localized at the terminal or satellite of chromosomes. The number of 5S rDNA were relatively stable, 74 of the varieties investigated contained 6 sites, located at the terminal of chromosomes and near centromere. Only the Quanzishu 96 has 7 5S rDNA sites, and Yuzixiang 10 has 5 5S rDNA sites. In addition, rDNA analysis was also performed on two parents of Quanzishu 96. Both the two parents had 18 45S rDNA sites and 6 5S rDNA sites, which were different from the results of Quanzishu 96.Conclusions: For hexaploid sweet potato cultivars, there is genetic instability between purple-fleshed sweet potato cultivars. The 45S rDNA sites showed numerical variation, whereas conserved number of 5S rDNA sites were observed.

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Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes

Cited by 29 publications

References 40 publications

Origin, Diversity, and Evolution of Telomere Sequences in Plants

Origin, Diversity, and Evolution of Telomere Sequences in Plants

Chromosome numbers and polyploidy events in Korean non-commelinids monocots: A contribution to plant systematics

Comparative chromosomal localization of 45S and 5S rDNAs in 76 purple-fleshed sweet potato cultivars

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