title: TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
abstract: 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.
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Novák
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Laura
authors.initials: L
authors.lastname: Ávila Robledillo
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Andrea
authors.initials: A
authors.lastname: Koblížková
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Iva
authors.initials: I
authors.lastname: Vrbová
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Neumann
authors.affiliation: Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.
authors.forename: Jirí
authors.initials: J
authors.lastname: Macas
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D003196:Computer Graphics; D016384:Consensus Sequence; D029785:Cyperaceae / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D004276:DNA, Satellite / Q000145:classification / Q000235:genetics*; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D019684:Magnoliopsida / Q000235:genetics; D008677:Metaphase; D018532:Pisum sativum / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D031307:Vicia faba / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D018744:DNA, Plant; D004276:DNA, Satellite