title: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae).
abstract: We present the development of a genomic library using RADseq (restriction site associated DNA sequencing) protocol for marker discovery that can be applied on evolutionary studies of the sugarcane borer Diatraea saccharalis, an important South American insect pest. A RADtag protocol combined with Illumina paired-end sequencing allowed de novo discovery of 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from six individuals, representing 40 Gb of sequencing data. Approximately 1.7 Mb of the sugarcane borer genome distributed over 5289 minicontigs were obtained upon assembly of second reads from first reads RADtag loci where at least one SNP was discovered and genotyped. Minicontig lengths ranged from 200 to 611 bp and were used for functional annotation and microsatellite discovery. These markers will be used in future studies to understand gene flow and adaptation to host plants and control tactics.
authors: Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP, Brazil.|Ohio Agricultural Research and Development Center, Department of Entomology, Thorne Hall, The Ohio State University, 1680 Madison Avenue, Wooster, OH, USA.
authors: V A C
authors: VAC
authors: Pavinato
authors: Department of Genetics, University of São Paulo, Avenida Pádua Dias 11, CP 9, Piracicaba, SP, Brazil.
authors: G R A
authors: GRA
authors: Margarido
authors: Ohio Agricultural Research and Development Center, Molecular and Cellular Imaging Center, Selby Hall, The Ohio State University, 1680 Madison Avenue, Wooster, OH, USA.
authors: A J
authors: AJ
authors: Wijeratne
authors: Ohio Agricultural Research and Development Center, Molecular and Cellular Imaging Center, Selby Hall, The Ohio State University, 1680 Madison Avenue, Wooster, OH, USA.
authors: S
authors: S
authors: Wijeratne
authors: Ohio Agricultural Research and Development Center, Molecular and Cellular Imaging Center, Selby Hall, The Ohio State University, 1680 Madison Avenue, Wooster, OH, USA.
authors: T
authors: T
authors: Meulia
authors: Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP, Brazil.
authors: A P
authors: AP
authors: Souza
authors: Ohio Agricultural Research and Development Center, Department of Entomology, Thorne Hall, The Ohio State University, 1680 Madison Avenue, Wooster, OH, USA.
authors: A P
authors: AP
authors: Michel
authors: Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP, Brazil.|Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of São Paulo (APTA), Rodovia SP 127 km 30, CP 28, Piracicaba, SP, Brazil.
authors: M I
authors: MI
authors: Zucchi
mesh_terms: D000818:Animals; D004247:DNA; D005819:Genetic Markers; D049750:Genome, Insect; D007915:Lepidoptera / Q000235:genetics*; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D031786:Saccharum; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D004247:DNA
keywords: Population genomics; ecological adaptation; mbRADseq; single-nucleotide polymorphism (SNP) 