Davey et al, 2013

As indicated in Davey et al, 2013, repeat annotation was performed on both the Pahang A-genome and the PKW consensus B-genomes as well as de novo assembled contigs with Repeat Masker V4.0.3 software tool using RMBLAST 2.2.27 as the engine and using the customized library of M. acuminata repeats (1903 sequences) from Hribova et al. 2010.

3,540 gene models were annotated as TE. 284 addtional gene models were predicted as TE based on the combination of 4 different approaches.

• list of keywords provided with the annotation ( transposons, retrotransposons, gag pol, transposase, reverse transcriptase, polyprotein, copia)
• list of IPR domains related to TE IPR000123, IPR003545, IPR013103,IPR000477,IPR003036,IPR002079,IPR004004,IPR004028,IPR004957 , IPR003141, IPR005162, IPR000721, IPR014817,IPR014834, IPR016195, IPR015699, IPR004312, IPR001584,IPR004332,IPR018289
• blast search on repbase (1e-10, 80% query coverage)
• Blast search on a custom database made from DH Pahang (1e-10, 100% query coverage) Any hit presnet in 3 out of the 4 methods was filtered.