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

Abstract

Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, 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 analysing 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.

A chromosome-level haplotype-resolved genome assembly of oriental tobacco budworm (Helicoverpa assulta)

“…To verify the completeness of our genome chromosome assembly, we conducted an analysis of telomere repeat sequences on each chromosome based on the genome repeat sequence annotation results. Initially, we analyzed the telomere repeat motif sequences of Lepidoptera insects in TeloBase 58 , and we found that the majority of repeat motifs ranged from 5 to 9 bp in length, and (TTAGG)n/(CCTAA)n is the main motif in telomeres. After that, we identified regions within 15 kb at both ends of the chromosomes in our results where the length of repeat sequences exceeded 1k,and the repeat motif sequence ranged from 5 to 9 bp.…”

Telomere Length Variation in Model Bryophytes

“…Evaluation of WGS data through the TeloBase database [27] indicated that C. purpureus harbors the canonical plant-like telomere repeat, TTTAGGG. We analyzed TL in four natural isolates of C. purpureus collected from three different geographical locations: R40 (male strain, New York, USA), GG1 (female strain, Austria), B150 and B190 (female and male lines, respectively, Alaska, USA).…”

“…Unlike the situation with the flowering plants [27,28], very few bryophyte species have previously been investigated for specific features of telomere biology. All bryophytes analyzed so far harbor the canonical Arabidopsis-type telomere repeats TTTAGGG [29][30][31][32], and in a few species, the composition of telomeric repeats can be deciphered from the whole-genome sequencing data [18,20,33,34].…”

Unwrap RAP1’s Mystery at Kinetoplastid Telomeres

“…Telomeres are nucleoprotein complexes located at chromosome ends [1]. In most eukaryotes, the telomere contains simple repetitive sequences, such as (TTAGGG) n in vertebrates, with the G-rich strand going 5 ′ to 3 ′ toward the chromosome end [2,3]. Although most parts of the telomere are double-stranded, the very end of the telomere has a single-stranded 3 ′ overhang [4,5].…”