TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

0479687 - BC 2018 RIV GB eng J - Journal Article
Novák, Petr - Ávila Robledillo, Laura - Koblížková, Andrea - Vrbová, Iva - Neumann, Pavel - Macas, Jiří
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Nucleic Acids Research. Roč. 45, č. 12 (2017), č. článku e111. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR GBP501/12/G090; GA MŠMT(CZ) LM2015047
Institutional support: RVO:60077344
Keywords : in-situ hybridization * repetitive sequences * tandem repeats * vicia-faba
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 11.561, year: 2017

Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
Permanent Link: http://hdl.handle.net/11104/0275655