Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

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, distribution, 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 grasshopper 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 association 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 elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.

Chromosomal Mapping of Repetitive DNAs in <b><i>Characidium</i></b> (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes

“…In general, both di-and trinucleotides were widely and similarly distributed in the genomes of the analyzed species, with a preferential accumulation in subtelomeric areas. In fact, it has been postulated that microsatellite accumulation in eukaryotic genomes is nonrandom and that each group of organisms/species show preferential accumulation of specific SSR motifs with a particular chromosomal distribution [Tóth et al, 2000;Ruiz-Ruano et al, 2015]. The (CA) 15 , (GA) 15 and (CG) 15 SSRs were previously mapped in different characiform fishes and had similar subtelomeric distributions in Hoplias , Leporinus and Triportheus species, while 2 Semaprochilodus species showed few centromeric/subtelomeric signals [Cioffi et al, 2011[Cioffi et al, , 2012Poltronieri et al, 2013;Terencio et al, 2013;Yano et al, 2014].…”

“…Together, these mechanisms control the expansion, accumulation and elimination of these sequences at different levels of resolution (e.g. interspecific, interpopulational and/or intragenome) [Dover, 1993;McMurray, 1995;Hancock, 1996, Milani andCabral-de-Mello, 2014;Ruiz-Ruano et al, 2015]. We also investigated the genomic location of minor and major ribosomal DNAs in the C .…”

“…Our results revealed variability in the distribution of repetitive DNA sequences and their possible association with sex chromosome diversification in Characidium species. © 2015 S. Karger AG, Basel korná et al, 2011; Kejnovský et al, 2013;Milani and Cabral-de-Mello, 2014;Ruiz-Ruano et al, 2015;Ziemniczak et al, 2014]. In this context, cytogenetic studies have provided a better characterization of sex chromosomes by identifying distinctive degrees of heterochromatinization and differential accumulation of repetitive sequences [for a review, see .…”

High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

“…In addition, a recent study of two other grasshopper species showed by fluorescent in situ hybridization that microsatellites are strongly associated with repetitive elements including histone gene spacers, ribosomal DNA intergenic spacers and transposable elements (Ruiz‐Ruano et al. 2014). …”

High-throughput analysis of the satellitome illuminates satellite DNA evolution

“…However, as in other sequenced genomes, information about the repetitive components of the genome is rather scarce, especially for satDNA. We have recently reported microsatellite content in L. migratoria at both genomic and cytogenetic levels12, but the search for satDNAs through the classical restriction endonuclease digestion and electrophoresis approach failed in this species (MD López-León and P Lorite, personal communication). Up to now, only 21 satDNAs have been reported in 12 orthopteran species, most of them grasshoppers (Supplementary Table S1).…”