A bioinformatics approach to identify telomere sequences

BioTechniques
Indira Somanathan, Chris Baysdorfer

Abstract

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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Citations

Jun 25, 2020·Genome Biology and Evolution·Ruihao ShuQilian Qin
Mar 11, 2020·Frontiers in Plant Science·Vratislav Peska, Sònia Garcia
Nov 17, 2021·The Plant Journal : for Cell and Molecular Biology·Priyanka SharmaRobert J Henry

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Datasets Mentioned

BETA
SRX3381811
SRX3381814
and
SRX3381816
SRX3381815
SRX3381813
SRX3381817

Methods Mentioned

BETA
confocal microscopy
Fluorescence
PCR

Software Mentioned

SeqMan NGen
Ion Torrent
SERF

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