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 Il...

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Bibliographic Details
Published in:Molecular ecology resources 2017-05, Vol.17 (3), p.454-465
Main Authors: Pavinato, V. A. C., Margarido, G. R. A., Wijeratne, A. J., Wijeratne, S., Meulia, T., Souza, A. P., Michel, A. P., Zucchi, M. I.
Format: Article
Language:English
Subjects:
Animals
Assembly
Biological evolution
Borers
Deoxyribonucleic acid
Diatraea saccharalis
DNA
DNA sequencing
ecological adaptation
Gene flow
Genetic Markers
Genome, Insect
Genomes
Host plants
Insects
Lepidoptera - genetics
Libraries
Markers
mbRADseq
Microsatellite Repeats
Polymorphism, Single Nucleotide
Population genomics
Saccharum
Sequence Analysis, DNA
Single-nucleotide polymorphism
single‐nucleotide polymorphism (SNP)
Sugarcane
Tactics
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Summary: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.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.12583