Identification of Whole Genome Segmental Duplications

The strategy used to detect segmental duplications (SDs) was based on the WGAC (whole genome assembly comparison) method. Self-BLAST searches were performed for all assembled contig sequences. Sequences with ≥90% identity over a ≥1000 bp alignment length were considered possible SDs. Self-hits, duplicate entries, and partial and reverse BLAST hits were removed to obtain the final list and the amount of SDs in the genome. Sequences of SDs were extracted from whole assemblies using PERL scripts and then subjected to FGENESH and MapRep in MolQuest 2.2 Software, for the prediction of genes and transposable elements, respectively. Predicted genes were self-BLAST searched and parsed to remove duplicates, and partial and redundant genes. Genes were BLAST searched against the NCBI nr database for functional annotation.