Transcriptome of the Traditional Coconut Variety Laguna Tall.

Coconut, Cocos nucifera L., is widely cultivated for its edible and non-edible products. In the Philippines, the traditional coconut variety, Laguna Tall (LAGT), exhibits good genetic potential as a pure population or as open-pollinated variety (OPV). It was the male parent of the first PCA-recommended hybrid. Because of its importance in agronomic breeding, efforts are geared towards increasing genetic resources through genome and transcriptome sequencing. Here, pooled total RNA from leaves, nuts, and flowers of mature stage LAGT was sequenced using Illumina HiSeq 2000, followed by de novo assembly using four different transcriptome assemblers: Trinity, SOAPdenovo-Trans, Trans-Abyss, and Velvet-Oases. Each assembly was evaluated for accuracy using RSEM-EVAL, a reference-free evaluation method for transcript abundance data. Trans-Abyss outperformed the other three assemblers, but to have a better representation of the LAGT transcriptome, assemblies generated by the four programs were combined using the Evidential Gene tr2aacds pipeline. A total of 79,263 transcripts were generated from the combined transcriptomes. Also, Fragments Per Kilobase of transcript per Million mapped read (FPKM) units were used to quantify in silico gene expression. A total of 68,147 transcripts were generated by RSEM and compared against the CDD, Trembl, and UniProt databases. Gene ontology (GO) analysis and KEGG classification revealed that up to 33.8% of LAGT genes are involved in protein modification. The top 20 expressed genes were annotated using the nr database, which revealed that the most highly expressed transcript is a novel transcript. Microsatellite markers were also obtained for future use as breeding tools. Overall, this study provides a comprehensive assembly of the Cocos nucifera L. transcriptome useful as a molecular toolbox to identify key factors involved in important biological and cellular processes in coconut. [ABSTRACT FROM AUTHOR]