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Restriction site associated DNA ( RAD ) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)
Author(s) -
Pavinato V. A. C.,
Margarido G. R. A.,
Wijeratne A. J.,
Wijeratne S.,
Meulia T.,
Souza A. P.,
Michel A. P.,
Zucchi M. I.
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12583
Subject(s) - diatraea saccharalis , crambidae , biology , lepidoptera genitalia , botany , dna , microbiology and biotechnology , genetics
We present the development of a genomic library using RAD seq (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 RAD tag protocol combined with Illumina paired‐end sequencing allowed de novo discovery of 12 811 SNP s 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 RAD tag 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.