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.

Základní údaje

Originální název

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

Autoři

LYČKA, Martin (203 Česká republika, domácí), Michal BUBENÍK (203 Česká republika, domácí), Michal ZÁVODNÍK (203 Česká republika, domácí), Vratislav PESKA, Petr FAJKUS (203 Česká republika, domácí), Martin DEMKO (703 Slovensko, domácí), Jiří FAJKUS (203 Česká republika, domácí) a Miloslava FOJTOVÁ (203 Česká republika, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

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

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 14.900 v roce 2022

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

001051997800001

Klíčová slova anglicky

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

Štítky

CF BIOIT, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 7. 8. 2024 14:01, prof. RNDr. Jiří Fajkus, CSc.

Anotace

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.

Návaznosti

GX20-01331X, projekt VaV

Název: Biogeneze a evoluce telomerázy u rostlin

Investor: Grantová agentura ČR, Biogenesis and evolution of telomerase in plants

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

90255, velká výzkumná infrastruktura

Název: ELIXIR CZ III

90267, velká výzkumná infrastruktura

Název: NCMG III

Citovat

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

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