Survey of Arabidopsis- and Human-type Telomere Repeats in Plants Using Fluorescence in situ Hybridisation

Shibata, Fumiaki; Hizume, Masahiro

doi:10.1508/cytologia.76.353

Cited by 16 publications

(27 citation statements)

References 31 publications

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“…In addition, other publications have been consulted, addressing telomere composition in relatively large datasets representing different plant groups (i.e. Thomas et al 1996;Adams et al 2001;Sýkorová et al 2003aSýkorová et al , 2003bSuzuki, 2004;Shibata and Hizume, 2011). Different telomere sequences have been considered, namely: Arabidopsis-type, Allium-type, Cestrum-type, Bombyx-type, Human-type, Oxythricha-type and Tetrahymena-type.…”

Section: New Data Included: Telomere Composition and Sequenced Plant mentioning

confidence: 99%

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

et al. 2017

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Here we present the third release of the plant rDNA database (March 2017), an open access online resource with information on numbers, locations and structure of 5S and 18S-5.8S-26S (35S) ribosomal DNA (rDNA) (www.plantrdnadatabase.com). Data are now available for 2,148 species (3,783 entries), extracted from 785 papers published until the end of 2016. This means an expansion of 33.5% in terms of new species and 13% in new publications consulted. We appreciate an increased interest on rDNA loci research in recent years, since 10.78% of all data available were published only in 2016. The database has been expanded to include information on telomere composition and on species whose genome has been fully sequenced up to date. Telomere sequence is only known with certainty for 9.60% of species in the database and for 36.79% at the genus level, indicating, potentially, that the consensus plant telomere (Arabidopsis-type) might not be as extended as previously thought. We have also introduced the taxonomic category order as an additional option for data browsing. Similarly, we have included a new category to indicate the hybrid status of taxa. In addition, we upgraded and/or proofread tabs and links and slightly modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments.

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Section: New Data Included: Telomere Composition and Sequenced Plant mentioning

confidence: 99%

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

et al. 2017

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“…Hence, SERF analysis primarily utilized the raw NGS data on all of the additional species investigated here. The analysis of multiple species (Table 4) has either reinforced earlier findings [29,38,39,42,43] or identified other potential telomere repeat motifs bioinformatically, requiring further cytological confirmation.…”

Section: Resultsmentioning

confidence: 57%

“…Later studies, however, did suggest the presence of these two types of telomere repeat motifs with an abundance of the human-type in Narcissus triandrus and Muscari neglectum telomeres [39]. SERF analysis on N. jonquilla 's raw NGS data sets identified a 15bp unique conserved tandem repeat motif (GAGGGTGCACTCACG) on a read with a high quality metric (90) in addition to the human-type telomere repeat motif (TTAGGG) with 90 (Table 5).…”

Section: Resultsmentioning

confidence: 99%

A Bioinformatics Approach to Identify Telomere Sequences

Somanathan

Baysdorfer

2018

BioTechniques

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Conventional approaches to identify a telomere motif in a new genome are laborious and time-intensive. An efficient new methodology based on next-generation sequencing (NGS), de novo sequence repeat finder (SERF) and fluorescence in situ hybridization (FISH) is presented. Unlike existing heuristic approaches, SERF utilizes an exhaustive analysis of raw NGS reads or assembled contigs for rapid de novo detection of conserved tandem repeats representing telomere motifs. SERF was validated using the NGS data from Ipheion uniflorum and Allium cepa with known telomere motifs. The analysis program was then used on NGS data to investigate the telomere motifs in several additional plant species and together with FISH proved to be an efficient approach to identify as yet unknown telomere motifs.

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“…In this, a useful experimental approach, developed first for human cells, is the Telomere Repeat Amplification Protocol (TRAP) (Kim et al, 1994), followed by sequencing of the detected products (Peska et al, 2015;Fajkus et al, 2016), which is a little less sensitive to false-positive results than FISH. All these methods, including FISH (Fuchs et al, 1995;Shibata and Hizume, 2011) and others such as slot-blot hybridization (Sykorova et al, 2003c), and TRAP (Fulneckova et al, 2012;Fulneckova et al, 2016), can be used to screen for telomeres across wide groups of complex organisms, including plants. However, only a combination of suitably chosen methods can convincingly lead to a conclusion about the telomere function of a candidate sequence, since results base on a single approach might be misleading.…”

Section: From Screenings To Discovery: How Telomeric Motifs Can Be Idmentioning

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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Survey of Arabidopsis- and Human-type Telomere Repeats in Plants Using Fluorescence in situ Hybridisation

Cited by 16 publications

References 31 publications

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

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

A Bioinformatics Approach to Identify Telomere Sequences

Origin, Diversity, and Evolution of Telomere Sequences in Plants

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