**1. Introduction**

Repetitive DNA often constitutes the majority of grass genomes, but these repeated segments vary extensively from species to species in absolute amounts, sequences, and dispersion patterns [1]. Due to the rapid evolution and characteristic genomic distribution patterns, repetitive sequences have been useful for phylogenetic analysis and chromosomal identification, as well as for studying nuclear architecture [2,3]. According to the length of the repeated units and array size, tandem repeated DNA sequences can be classified into three groups, including microsatellites, mini-satellites, and satellite DNA. The mini-satellites (10–60 bp) were first described by Jeffreys et al. [4], and are usually defined as the repetition in tandem of a short (6- to 100-bp) motif spanning 0.5 kb to several kilobases [5,6]. Mini-satellites were first characterized in the human genome [4], where they share a common motif known as the core sequence [7], and were subsequently discovered in a variety of plant species [8–11]. A remarkable advance in the knowledge of repetitive sequences has occurred in recent years because of the introduction of next-generation sequencing technologies [12]. Bioinformatic pipelines or web servers have provided computational facilities for the identification of mini-satellites for next-generation sequence data [13–15]. The availability of genome sequences allows

the development of site-specific mini-satellites, as has been reported for diploid and polyploid plant species [16–19].

Bread wheat, *Triticum aestivum* L., consists of three closely related subgenomes (A, B, D), and these genomes contain a high proportion (>85%) of repetitive DNA [20,21]. Universal repetitive sequences and genome-specific repetitive sequence families have been identified in Triticeae species [22]. The mini-satellite sequences in wheat and related species have been referred to as "variable number tandem repeats" (VNTRs). The identified mini-satellite sequences in *T. aestivum*, *T. durum* Desf., *T. monococcum* L., *Aegilops speltoides* Tausch, and *Ae. tauschii* Coss. have shown a high degree of polymorphism among the various genomes [23,24]. Probes and markers for mini-satellites have been successfully used for DNA fingerprinting [11]. Extensive analysis of such mini-satellite tandem repeats is potentially useful for combining genomic and cytogenetic studies of wheat chromosomes.

The recent completion of the genomic sequencing of *T. aestivum* cv. Chinese Spring (International Wheat Genome Sequencing Consortium, [25]), and also the A genome donor (*Triticum urartu* Thumanjan ex Gandilyan) [26], the D genome progenitor (*Ae. tauschii*) [27], and the tetraploid wheat, *Triticum dicoccoides* Schrank ex Schübl. (AABB genomes [28]), provide opportunities for the localization of repetitive sequences to chromosome physical regions. Lang et al. [29] first constructed a database of repeats according to unit size, array number, and physical coverage length of TRs in the wheat genome. The comparison of tandem repeats, including satellite repeats, at genome-wide levels may potentially shed new light on our understanding of genomic amplification through evolutionary processes [3,29,30].

The principal aim of the present study is to describe the physical location and sequence variations of a novel mini-satellite repeat, Ta-3A1, between wheat and its ancestors by genome-wide analysis. Fluorescence in situ hybridization by Ta-3A1 for chromosome identification and evolution of wheat and related species is also discussed.
