|
|||||
|
|
Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer,Diatraea saccharalis Fab. (Lepidoptera: Crambidae) |
|
| Authors: | V. A. C. Pavinato G. R. A. Margarido A. J. Wijeratne S. Wijeratne T. Meulia A. P. Souza A. P. Michel M. I. Zucchi |
| Affiliation: | 1. Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil;2. Ohio Agricultural Research and Development Center, Department of Entomology, Thorne Hall, The Ohio State University, Wooster, OH, USA;3. Department of Genetics, University of S?o Paulo, Piracicaba, SP, Brazil;4. Ohio Agricultural Research and Development Center, Molecular and Cellular Imaging Center, Selby Hall, The Ohio State University, Wooster, OH, USA;5. Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of S?o Paulo (APTA), Piracicaba, SP, Brazil |
| 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. |
| Keywords: | ecological adaptation mbRADseq Population genomics single‐nucleotide polymorphism (SNP) |