<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>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 <italic>de novo</italic> library in genome annotation and gene prediction was assessed in comparison with the conventional libraries (Dfam+RepBase), using RepeatMasker. <italic>De novo</italic> 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 <italic>de novo</italic> library can be accessed at <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.kau.in/repeat-libraries">http://www.kau.in/repeat-libraries</ext-link>.</p>
</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.

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

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Even though repeat masking using custom designed libraries significantly improves the genome annotation and gene prediction, such libraries for palm trees are...

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

Published Online: Jul 16, 2023

Page range: 114 - 117

DOI: https://doi.org/10.2478/sg-2023-0011

Keywords
Genome sequencing, NGS, Arecaceae,

© 2023 Shri Hari Prasad et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Supplementary Material Details

Supplementary Material Details

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

Published Online: Jul 16, 2023

Page range: 114 - 117

DOI: https://doi.org/10.2478/sg-2023-0011

KeywordsGenome sequencing, NGS, Arecaceae,

© 2023 Shri Hari Prasad et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Supplementary Material Details

Supplementary Material Details

Keywords
Genome sequencing, NGS, Arecaceae,