Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

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.

[1]  D. Bolnick,et al.  Demystifying the RAD fad , 2014, Molecular ecology.

[2]  Gordon Luikart,et al.  Trade‐offs and utility of alternative RADseq methods: Reply to Puritz et al. , 2014, Molecular ecology.

[3]  M. Solís,et al.  Geographic Population Structure of the Sugarcane Borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), in the Southern United States , 2014, PloS one.

[4]  M. Ruvolo-Takasusuki,et al.  Population genetics of the sugarcane borer Diatraea saccharalis (Fabr.) (Lepidoptera: Crambidae) , 2014 .

[5]  Åke Brännström,et al.  Genomics and the origin of species , 2014, Nature Reviews Genetics.

[6]  Angel Amores,et al.  Stacks: an analysis tool set for population genomics , 2013, Molecular ecology.

[7]  M. Zucchi,et al.  Development and characterization of microsatellite loci for genetic studies of the sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae). , 2013, Genetics and molecular research : GMR.

[8]  A. Amores,et al.  Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences , 2011, G3: Genes | Genomes | Genetics.

[9]  M. Blaxter,et al.  Genome-wide genetic marker discovery and genotyping using next-generation sequencing , 2011, Nature Reviews Genetics.

[10]  Pascal Frey,et al.  High‐throughput microsatellite isolation through 454 GS‐FLX Titanium pyrosequencing of enriched DNA libraries , 2011, Molecular ecology resources.

[11]  J. Galindo,et al.  Applications of next generation sequencing in molecular ecology of non-model organisms , 2011, Heredity.

[12]  A. Meyer,et al.  Adaptation in the age of ecological genomics: insights from parallelism and convergence. , 2011, Trends in ecology & evolution.

[13]  Robert J. Elshire,et al.  A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species , 2011, PloS one.

[14]  P. Etter,et al.  Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads , 2011, PloS one.

[15]  J. Oakeshott,et al.  Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems , 2011, Evolutionary applications.

[16]  J. Ran,et al.  Structural characteristics and phylogenetic analysis of the mitochondrial genome of the sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae). , 2011, DNA and cell biology.

[17]  M. Blaxter,et al.  RADSeq: next-generation population genetics. , 2010, Briefings in functional genomics.

[18]  J. Slate,et al.  Adaptation genomics: the next generation. , 2010, Trends in ecology & evolution.

[19]  R. E. F. Munhoz,et al.  Genetic diversity analysis with RAPD linked to sex identification in the sugar cane borer Diatraea saccharalis. , 2010, Genetics and molecular research : GMR.

[20]  G. Luikart,et al.  Genomics and the future of conservation genetics , 2010, Nature Reviews Genetics.

[21]  V. Calcagno,et al.  Divergence in behaviour between the European corn borer, Ostrinia nubilalis, and its sibling species Ostrinia scapulalis: adaptation to human harvesting? , 2010, Proceedings of the Royal Society B: Biological Sciences.

[22]  J. Fordyce,et al.  Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies , 2010, Molecular ecology.

[23]  D. Crowder,et al.  Evolutionary ecology of insect adaptation to Bt crops , 2010, Evolutionary applications.

[24]  Nicholas Stiffler,et al.  Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags , 2010, PLoS genetics.

[25]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[26]  P. Etter,et al.  Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers , 2008, PloS one.

[27]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[28]  Jan van Oeveren,et al.  Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes , 2007, PloS one.

[29]  A. Amores,et al.  Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. , 2007, Genome research.

[30]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[31]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[32]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[33]  M. R. Thomas,et al.  Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. , 1994, BioTechniques.

[34]  D. Herms,et al.  The Dilemma of Plants: To Grow or Defend , 1992, The Quarterly Review of Biology.

[35]  J. W. Smith,et al.  Bibliography of the Neotropical Cornstalk Borer, Diatraea Lineolata (Lepidoptera: Pyralidae) , 1988 .

[36]  B. Uvarov.  Problems of Insect Ecology in Developing Countries , 1964 .

[37]  J. G. Myers.  The Ecological Distribution of some South American Grass and Sugar-cane Borers ( Diatraea spp., Lep., Pyralidae) , 1935 .

[38]  J. G. Myers.  The original Habitat and Hosts of three major Sugar-cane Pests of Tropical America ( Diatraea, Castnia and Tomaspis ) , 1932 .

[39]  S. D. Hensley,et al.  Insect Pests of Sugar Cane , 1972 .

[40]  H. Box.  Report upon Specimens of 'Diatræa' Guilding (Lepidoptera, Pyralidæ) in the Cornell University Collection , 1950 .

[41]  H. Box.  The more important Insect Pests of Sugar Cane in northern Venezuela. , 1950 .