Cleaned reads of sequenced libraries are available from European Nucleotide Archive (http://www.ebi.ac.uk/) under accessions PRJEB18101, PRJEB18102, PRJEB18103, PRJEB18104, PRJEB17691.
De novo assembly of the pooled cleaned reads was performed using Trinity based on chosen criteria.
Cleaned reads were assembled using a de novo genome assembly program Velvet v1.2.10 (Zerbino and Birney 2008).
Percentage of cleaned reads in parentheses.
All subsequent analyses were based on these cleaned reads.
The length of the cleaned reads peaked at 22 bp.
cproportion of cleaned reads uniquely mapped on CDS sequences.
dduplication rate estimated on 100 000 cleaned reads.
The cleaned reads were mapped by BWA [ 37].
Assembly of the cleaned reads from both sexes with NEWBLER and MIRA resulted in 96,379 contigs containing 87% of the cleaned reads.
bNumber of cleaned reads (percentage of all cleaned reads) containing an intact site for a methyl-insensitive restriction endonuclease more than 10 nucleotides from the ends.
