publication . Article . 2016

High-throughput analysis of the satellitome illuminates satellite DNA evolution

Josefa Cabrero; Francisco J. Ruiz-Ruano; Camacho JPM;
Open Access English
  • Published: 07 Jul 2016 Journal: Scientific Reports (issn: 2045-2322, Copyright policy)
  • Publisher: Nature Publishing Group
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 ...
Subjects
free text keywords: Multidisciplinary, Article
56 references, page 1 of 4

Kim Y. B.. Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel. P. Natl. Acad. Sci. USA 111, 10630–10635 (2014).

Tautz D. In DNA fingerprinting: State of the science (ed. Pena S. D.) Ch. 1, 21–28 (Birkhäuser Basel, 1993).

Richard G. F., Kerrest A. & Dujon B. Comp arative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol. Mol. Biol. R. 72, 686–727 (2008). [OpenAIRE]

Plohl M., MeštrovićN. & Mravinac B. Centromere identity from the DNA point of view. Chromosoma 123, 313–325 (2014).24763964 [OpenAIRE] [PubMed]

Lee H. R., Neumann P., Macas J. & Jiang J. Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice. Mol. Biol. Evol. 23, 2505–2520 (2006).16987952 [PubMed]

Usakin L.. Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176, 1343–1349 (2007).17409066 [OpenAIRE] [PubMed]

Kit S. J.Equilibrium sedimentation in density gradients of DNA preparations from animal tissues. J. Mol. Biol.3, 711–716 (1961).14456492 [OpenAIRE] [PubMed]

Britten R. J., Graham D. E. & Neufeld B. R. Analysis of repeating DNA sequences by reassociation. Methods Enzymol. 29, 363–405 (1974).4850571 [OpenAIRE] [PubMed]

Singer M.Highly repeated sequences in mammalian genomes. Int. J. Cytol.76, 67–112 (1982).

Novák P., Neumann P., Pech J., Steinhaisl J. & Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29, 792–793 (2013).23376349 [OpenAIRE] [PubMed]

Wang X.. The locust genome provides insight into swarm formation and long-distance flight. Nat. Commun.5, 2957 (2014).24423660 [OpenAIRE] [PubMed]

Ruiz-Ruano F. J., CuadradoÁ., Montiel E. E., Camacho J. P. M. & López-León M. D. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes. Chromosoma 124, 221–234 (2015).25387401 [PubMed]

Heckmann S.. The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. Plant J.73, 555–565 (2013).23078243 [PubMed]

Camacho J. P. M.. G-banding in two species of grasshoppers and it s relationship to C, N and fluorescence banding techniques. Genome 34, 638–643 (1991). [OpenAIRE]

FrydrychováR., Grossmann P., Trubac P., VítkováM. & Marec F. Phylogenetic distribution of TTAGG telomeric repeats in insects. Genome 47, 163–178 (2004).15060613 [PubMed]

56 references, page 1 of 4
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 ...
Subjects
free text keywords: Multidisciplinary, Article
56 references, page 1 of 4

Kim Y. B.. Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel. P. Natl. Acad. Sci. USA 111, 10630–10635 (2014).

Tautz D. In DNA fingerprinting: State of the science (ed. Pena S. D.) Ch. 1, 21–28 (Birkhäuser Basel, 1993).

Richard G. F., Kerrest A. & Dujon B. Comp arative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol. Mol. Biol. R. 72, 686–727 (2008). [OpenAIRE]

Plohl M., MeštrovićN. & Mravinac B. Centromere identity from the DNA point of view. Chromosoma 123, 313–325 (2014).24763964 [OpenAIRE] [PubMed]

Lee H. R., Neumann P., Macas J. & Jiang J. Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice. Mol. Biol. Evol. 23, 2505–2520 (2006).16987952 [PubMed]

Usakin L.. Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176, 1343–1349 (2007).17409066 [OpenAIRE] [PubMed]

Kit S. J.Equilibrium sedimentation in density gradients of DNA preparations from animal tissues. J. Mol. Biol.3, 711–716 (1961).14456492 [OpenAIRE] [PubMed]

Britten R. J., Graham D. E. & Neufeld B. R. Analysis of repeating DNA sequences by reassociation. Methods Enzymol. 29, 363–405 (1974).4850571 [OpenAIRE] [PubMed]

Singer M.Highly repeated sequences in mammalian genomes. Int. J. Cytol.76, 67–112 (1982).

Novák P., Neumann P., Pech J., Steinhaisl J. & Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29, 792–793 (2013).23376349 [OpenAIRE] [PubMed]

Wang X.. The locust genome provides insight into swarm formation and long-distance flight. Nat. Commun.5, 2957 (2014).24423660 [OpenAIRE] [PubMed]

Ruiz-Ruano F. J., CuadradoÁ., Montiel E. E., Camacho J. P. M. & López-León M. D. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes. Chromosoma 124, 221–234 (2015).25387401 [PubMed]

Heckmann S.. The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. Plant J.73, 555–565 (2013).23078243 [PubMed]

Camacho J. P. M.. G-banding in two species of grasshoppers and it s relationship to C, N and fluorescence banding techniques. Genome 34, 638–643 (1991). [OpenAIRE]

FrydrychováR., Grossmann P., Trubac P., VítkováM. & Marec F. Phylogenetic distribution of TTAGG telomeric repeats in insects. Genome 47, 163–178 (2004).15060613 [PubMed]

56 references, page 1 of 4
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