Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

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.

A simple non-toxic ethylene carbonate fluorescence in situ hybridization (EC-FISH) for simultaneous detection of repetitive DNA sequences and fluorescent bands in plants

“…Chromosome bands are higher-order genomic structures with epigenetic flavors, important to understand the functional aspects of genome organization (Holmquist 1992 ). They are usually not uniform in terms of sequence composition; thus, the information whether a given sequence belongs to a given band or how it is positioned in relation to the band is of prime interest (Robledillo et al 2018 ). Typically, to deduce the position of FISH signals in relation to banding, fluorescent differential staining and FISH are done separately on different slides or infrequently—sequentially on the same slide.…”

Adding color to a century‐old enigma: multi‐color chromosome identification unravels the autotriploid nature of saffron (Crocus sativus) as a hybrid of wild Crocus cartwrightianus cytotypes

“…Cluster analysis of low coverage read data is a well-established route for the development of chromosomal landmark probes in many plants (Heitkam et al, 2015;Weiss-Schneeweiss et al, 2015;Avila Robledillo et al, 2018). Like most plant genomes, Crocus genomes consist largely of repetitive DNA (Frello & Heslop-Harrison, 2000;Frello et al, 2004;Alavi-Kia et al, 2008) with hundreds of diverse repeat families, including retrotransposons, ribosomal DNA and the major satellite DNA families CroSat1-CroSat6.…”

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

“…On the other hand, the short‐read data are successfully utilized by bioinformatic pipelines specifically tailored to the identification of satellite repeats employing assembly‐free algorithms (Novák et al , ; Ruiz‐Ruano et al , ; Novák et al , ). Although these approaches proved to be efficient in satDNA identification and revealed a surprising diversity of satellite repeat families in some plant and animal species (Macas et al , ; Ruiz‐Ruano et al , ; Ávila Robledillo et al , ), they, in principle, could not provide much insight into their large‐scale arrangement in the genome. In this respect, the real breakthrough was recently made by the so‐called long‐read sequencing technologies that include the Pacific Biosciences and Oxford Nanopore platforms.…”