TeloBase: a community-curated database of telomere sequences
across the tree of life

J 2024

TeloBase: a community-curated database of telomere sequences across the tree of life

LYČKA, Martin, Michal BUBENÍK, Michal ZÁVODNÍK, Vratislav PESKA, Petr FAJKUS et. al.

Basic information

Original name

TeloBase: a community-curated database of telomere sequences across the tree of life

Authors

LYČKA, Martin (203 Czech Republic, belonging to the institution), Michal BUBENÍK (203 Czech Republic, belonging to the institution), Michal ZÁVODNÍK (203 Czech Republic, belonging to the institution), Vratislav PESKA, Petr FAJKUS (203 Czech Republic, belonging to the institution), Martin DEMKO (703 Slovakia, belonging to the institution), Jiří FAJKUS (203 Czech Republic, belonging to the institution) and Miloslava FOJTOVÁ (203 Czech Republic, belonging to the institution)

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2024, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

40402 GM technology , livestock cloning, marker assisted selection, diagnostics biomass feedstock production technologies, biopharming

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 14.900 in 2022

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkad672

UT WoS

001051997800001

Keywords in English

ASPERGILLUS-ORYZAE; PLANT; EVOLUTION; REPEATS; IDENTIFICATION; LOCALIZATION; CONSERVATION; CHROMOSOMES; ARABIDOPSIS; DIVERSITY

Abstract

V originále

Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. Ho we ver, currently available resources, Telomerase database' and Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by anal ysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/ telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality .To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.

Links

GX20-01331X, research and development project

Name: Biogeneze a evoluce telomerázy u rostlin

Investor: Czech Science Foundation

90254, large research infrastructures

Name: e-INFRA CZ II

90255, large research infrastructures

Name: ELIXIR CZ III

90267, large research infrastructures

Name: NCMG III

Citovat

LYČKA, Martin, Michal BUBENÍK, Michal ZÁVODNÍK, Vratislav PESKA, Petr FAJKUS, Martin DEMKO, Jiří FAJKUS and Miloslava FOJTOVÁ. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Research. Oxford: Oxford University Press, 2024, vol. 52, D1, p. "D311"-"D321", 11 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad672.

@article{2368536,
   author = {Lyčka, Martin and Bubeník, Michal and Závodník, Michal and Peska, Vratislav and Fajkus, Petr and Demko, Martin and Fajkus, Jiří and Fojtová, Miloslava},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gkad672},
   keywords = {ASPERGILLUS-ORYZAE; PLANT; EVOLUTION; REPEATS; IDENTIFICATION; LOCALIZATION; CONSERVATION; CHROMOSOMES; ARABIDOPSIS; DIVERSITY},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {TeloBase: a community-curated database of telomere sequences across the tree of life},
   url = {https://academic.oup.com/nar/article/52/D1/D311/7246534},
   volume = {52},
   year = {2024}
}

TY  - JOUR
ID  - 2368536
AU  - Lyčka, Martin - Bubeník, Michal - Závodník, Michal - Peska, Vratislav - Fajkus, Petr - Demko, Martin - Fajkus, Jiří - Fojtová, Miloslava
PY  - 2024
TI  - TeloBase: a community-curated database of telomere sequences across the tree of life
JF  - Nucleic Acids Research
VL  - 52
IS  - D1
SP  - "D311"-"D321"
EP  - "D311"-"D321"
PB  - Oxford University Press
SN  - 03051048
KW  - ASPERGILLUS-ORYZAE
KW  - PLANT
KW  - EVOLUTION
KW  - REPEATS
KW  - IDENTIFICATION
KW  - LOCALIZATION
KW  - CONSERVATION
KW  - CHROMOSOMES
KW  - ARABIDOPSIS
KW  - DIVERSITY
UR  - https://academic.oup.com/nar/article/52/D1/D311/7246534
N2  - Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. Ho we ver, currently available resources, Telomerase database' and Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by anal ysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/ telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality .To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
ER  -

LYČKA, Martin, Michal BUBENÍK, Michal ZÁVODNÍK, Vratislav PESKA, Petr FAJKUS, Martin DEMKO, Jiří FAJKUS and Miloslava FOJTOVÁ. TeloBase: a community-curated database of telomere sequences across the tree of life. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2024, vol.~52, D1, p.~''D311''-''D321'', 11 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad672.

Detailed Information on Publication Record