Abstract
Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.
Highlights
Satellite DNA is a class of repetitive DNA characterized by its genomic organization into long arrays of tandemly arranged units called monomers
We focus on the characterization of the satellite DNA population in the genome of Vicia faba, a species that has long served as a model for cytogenetic studies in plants[32,33,34]
Satellite DNA still represents one of the most enigmatic components of eukaryotic genomes, which is in part due to the technical difficulties associated with reliable characterization of a representative set of satellite repeats from the genomes of interest
Summary
Satellite DNA (satDNA) is a class of repetitive DNA characterized by its genomic organization into long arrays of tandemly arranged units called monomers. Novel sequencing technologies provide deep information about sequence composition of complex genomes of eukaryotes via generation of unprecedented amounts of sequence data These data can be utilized by bioinformatic pipelines tailored to the identification of satellite repeats from NGS reads without the need for their assembly[26,27,28,29]. Putative satellite repeats were identified based on the properties of cluster graphs obtained by similarity-based clustering of low-pass genome sequencing Illumina reads, as implemented in the RepeatExplorer pipeline[27] These graphs represent the reads and their sequence similarities as nodes and connecting edges, respectively, and form globular or ring-like shapes in the case of tandem repeats. We employed ChIP-seq analysis using CenH3 antibody to identify centromeric satellites, revealing their surprising diversity
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