High-throughput sequencing data reveals evolutionary conservation and differential transcription of satellites DNA among crickets species (Orthoptera; Gryllinae)

Abstract

Satellite DNA (satDNA) is a class of non-coding repetitive DNA abundant in most eukaryotic genomes. Mostly satDNAs constitute clustered arrays of tandemly repeated sequences located in the gene-poor heterochromatin of centromeres and telomeres. Moreover in some cases, they are also dispersed in eu/heterochromatin of sex chromosomes and as single or short arrays nearby protein-coding genes within euchromatin. Here we take advantages of DNA- and RNA-seq data from cricket’s species in order to perform a comparative analysis of content and expression of satDNAs. By graph-based clustering analysis of DNA-seq reads using RepeatExplorer software, dotplots analysis and FISH mapping we found that ~ 4% of the G. assimilis genome is represented by 13 A+T-rich satDNAs consisting of 11 well-defined families mainly located in the heterochromatic areas of chromosomes, and some of them able to form high-order repeats (HORs). In order to determine transcription profiles the raw RNA-seq reads from different tissues library of Gryllus species were mapped to each of the G. assimilis satDNAs using Bowtie2 and the method FPKM (fragments per kilo-base of transcript per million mapped reads) was used. The in silico transcriptional analysis of RNA-seq reads in G. assimilis, G. bimaculatus, G, firmus and G. rubens showed that some satDNAs are conserved in Gryllus species but differentially expressed in distinct tissues, sexes and besides tissue- and species-specific. In concordances with the transcriptional activity we found that G. assimilis satDNAs are also capable to adopt RNA secondary structures with well-defined helices ranging from 2 bp to 7 bp lengths. The folding possibility forming secondary structure helps to the satDNA dispersion along the genome by rolling-circle replication mechanism, in which circular monomer result from secondary structure RNA processing into linear monomers and subsequently circularization by a host-specific RNA ligase. The conservation of expression for different satDNAs in Gryllus species suggests a functional role for these sequences, as observed in other insects. Our data suggests functional roles of satDNAs for sexual differentiation at the chromatin levels, heterochromatin formation and centromeric function.