Abstract
Satellite DNA (satDNA) is a major component yet the great unknown of eukaryote genomes and clearly underrepresented in genome sequencing projects. Here we show the high-throughput analysis of satellite DNA content in the migratory locust by means of the bioinformatic analysis of Illumina reads with the RepeatExplorer and RepeatMasker programs. This unveiled 62 satDNA families and we propose the term “satellitome” for the whole collection of different satDNA families in a genome. The finding that satDNAs were present in many contigs of the migratory locust draft genome indicates that they show many genomic locations invisible by fluorescent in situ hybridization (FISH). The cytological pattern of five satellites showing common descent (belonging to the SF3 superfamily) suggests that non-clustered satDNAs can become into clustered through local amplification at any of the many genomic loci resulting from previous dissemination of short satDNA arrays. The fact that all kinds of satDNA (micro- mini- and satellites) can show the non-clustered and clustered states suggests that all these elements are mostly similar, except for repeat length. Finally, the presence of VNTRs in bacteria, showing similar properties to non-clustered satDNAs in eukaryotes, suggests that this kind of tandem repeats show common properties in all living beings.
Highlights
Eukaryote genomes are plenty of repetitive elements including transposable elements (TEs), tandem repeats, segmental duplications, ribosomal DNA, multi-copy gene families, pseudogenes, etc. which, collectively, constitute the repeatome[1]
Today this technique is not performed to search for Satellite DNA (satDNA), since it was replaced by other techniques such as DNA renaturation kinetics[8], restriction digestion and electrophoresis yielding a ladder pattern[9] and, most recently, by the bioinformatic analysis of a huge collection of short DNA sequences yielded by Generation Sequencing (NGS)[10]
In the first run of RepeatExplorer (RE), performed in parallel on Illumina reads from the SL and NL individuals, we found 26 and 21 satDNAs, respectively
Summary
Eukaryote genomes are plenty of repetitive elements including transposable elements (TEs), tandem repeats, segmental duplications, ribosomal DNA, multi-copy gene families, pseudogenes, etc. which, collectively, constitute the repeatome[1]. The name “satellite DNA” is historical since this kind of repetitive DNA was discovered as a small peak in the CsCl ultracentrifugation profile[7] Today this technique is not performed to search for satDNA, since it was replaced by other techniques such as DNA renaturation kinetics[8], restriction digestion and electrophoresis yielding a ladder pattern[9] and, most recently, by the bioinformatic analysis of a huge collection of short DNA sequences yielded by Generation Sequencing (NGS)[10]. By means of stepwise clustering of repetitive DNA10 intermingled by substraction of the repetitive elements found in previous steps, we found that the satellitome of L. migratoria consists of, at least, 62 different satDNAs with monomer size ranging between 5 and 400 bp This procedure allowed detection of many poorly abundant satDNAs which would have gone unnoticed through conventional methods. This broad catalog of different satDNA families allowed an analysis for general features which provided new insights on the origin and evolution of this part of the repeatome
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