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Transcriptome of the Traditional Coconut Variety Laguna Tall

Ma. Regina Punzalan1,2, Ma. Anita Bautista1,2, Ernesto Emmanuel3,
Ramon Rivera3, Susan Rivera3, and Cynthia Saloma1,2*

1Philippine Genome Center (PGC), University of the Philippines,
Diliman, Quezon City 1101 Philippines
2National Institute of Molecular Biology and Biotechnology,
University of the Philippines, Diliman, Quezon City 1101 Philippines
3Philippine Coconut Authority – Zamboanga Research Center (PCA-ZRC),
San Ramon, Zamboanga City 7000 Philippines

*Corresponding Author: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 


ABSTRACT

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.

 

INTRODUCTION

Coconut is an economically significant crop in the tropics particularly in the Philippines, Indonesia, and India. Commonly referred to as the “Tree of Life,” this palm is widely cultivated in 93 countries and is globally a source of edible and non-edible products such as copra, desiccated coconut, coconut oil, coco lumber, and coco coir (Arancon 2010). The Philippines is the top exporter of coconut in the world, with coconut exports accounting to USD 1,586 million per year – equivalent to 30% of the country’s total agricultural earnings (Forbes 2013). In 2018, the country exported 350,000 metric tons of copra and 1 million metric tons of coconut oil (Index Mundi 2019). More than 3.5 M hectares of agricultural land are utilized as coconut plantation with an average production of 14.9 billion nuts per year (PCA 2019). The yield of coconut palms depends on many factors: interaction of the variety; the growing environment, particularly soil conditions and climate; cultural practices such as fertilizer application, pest, and disease management; and farming systems. In terms of varieties, the Philippines has several that are used in commercial planting. Among these is LAGT, which is one of the major tall populations grown in the country (Santos and Rivera 1994). It was named as . . . read more


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