An efficient repeat masking library for the genomic data of coconut and related trees

Abstract

Even though repeat masking using custom designed libraries significantly improves the genome annotation and gene prediction, such libraries for palm trees are yet to be designed and made accessible to the researchers. In this study, a repeat library was designed and validated for use in coconut and related palm genomes. Coconut genome with chromosome-level assembly was used to design independent libraries for tall and dwarf ecotypes, which were subsequently merged. Efficiency of the combined de novo library in genome annotation and gene prediction was assessed in comparison with the conventional libraries (Dfam+RepBase), using RepeatMasker. De novo library had 76.3 % efficiency in coconut genomes compared to 3.51 % in custom libraries and number of genes predicted was reduced from an average of 193,099 to 31,022. In date palm, oil pam and sago palm also, combined library gave higher repeat masking and reduced the number of genes predicted. The de novo library can be accessed at http://www.kau.in/repeat-libraries.