RESEARCH ARTICLE Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes Francisco J. Ruiz-Ruano & Ángeles Cuadrado & Eugenia E. Montiel & Juan Pedro M. Camacho & María Dolores López-León Received: 28 June 2014 /Revised: 17 October 2014 /Accepted: 29 October 2014 # Springer-Verlag Berlin Heidelberg 2014 Abstract Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, dis- tribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshop- per species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and associa- tion with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile ele- ments in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster. Introduction Microsatellite DNA (or SSRs: simple sequence repeats) is an abundant class of repetitive DNA composed of tandemly arranged short repeated motifs of 1 to 6 bp and being widely distributed in plant and animal genomes (Tautz and Renz 1984; Tóth et al. 2000; Zane et al. 2002; Cuadrado and Jouve 2007a, 2011). Studies using microsatellites have been mainly focused on their use as polymorphic markers in population genetics, genetic diversity, or kinship contexts (reviewed in Schlötterer and Pemberton 1998; Goldstein and Schlötterer 1999). This is particularly true in insects, where reports based on SSR molecular variation are abundant (Insuan et al. 2007; Agustinos et al. 2011; Blondin et al. 2013; Manrique-Poyato et al. 2013). In recent years, microsatellite genomic analysis has been powered by the development of high throughput next generation sequencing (NGS) technologies, based on massive sequencing approaches which enable a rapid, low-cost, and low time-consuming way to characterize microsatellites (Malausa et al. 2011; Iquebal et al. 2013). This technology is nowadays particularly interesting for nonmodel species (Meglécz et al. 2012; Hunter and Hart 2013; Schoebel et al. 2013), as it allows a global description of repetitive DNAs, including the microsatellite fraction. Much less is known about microsatellite chromosomal dis- tribution, even though its knowledge is critical for addressing key issues such as chromosome origin, organization, structure, function, and evolution. Moreover, precise chromosomal iden- tification may be based on specific SSR distribution pattern, as is the case in barley where chromosome distribution of (AAG) 5 and (ACT) 5 microsatellite repeats allows easy chromosome identification and detection of structural chromosome rear- rangements (e.g., translocations) (Carmona et al. 2013). Drosophila is one of the few animals where microsatellites have been profusely analyzed at the chromosomal level (Cuadrado and Jouve 2007b, 2011; Santos et al. 2010). Electronic supplementary material The online version of this article (doi:10.1007/s00412-014-0492-7) contains supplementary material, which is available to authorized users. F. J. Ruiz-Ruano : E. E. Montiel : J. P. M. Camacho : M. D. López-León (*) Departamento de Genética Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain e-mail: mdlopez@ugr.es Á. Cuadrado Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain Chromosoma DOI 10.1007/s00412-014-0492-7