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GENERATING TRANSCRIPTOME SEQUENCE INFORMATION FROM Cocos nucifera L. ‘CATIGAN GREEN DWARF’ CULTIVAR

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  • Create Date December 6, 2019
  • Last Updated June 18, 2020

GENERATING TRANSCRIPTOME SEQUENCE INFORMATION FROM Cocos nucifera L. ‘CATIGAN GREEN DWARF’ CULTIVAR

Bautista MAM, Acoba DJ, Emmanuel EE, Rivera RL, Rivera SM3 Saloma CP

ABSTRACT

The Philippines is one of the leading producers of coconut worldwide. To sustain or increase production, varietal improvement is warranted and can be accelerated through molecular breeding. However, genomic resources remain limited for coconuts. This study aims to expand these resources by sequencing and assembling the transcriptome of tissues from ‘Catigan Green Dwarf’ (CATD) cultivar. Transcript clustering by Corset produced 92,840 unigenes in endosperm, 48,547 in endocarp, 45,160 in mesocarp, 51,635 in leaf, 65,996 in female flower, and 60,534 in male flower. Assessment by RMBT (reads mapped back to transcripts) revealed that 69 to 78% of the reads aligned to the assembly. Analysis by BUSCO suggests that tissue assemblies recover 72 to 81% of highly conserved orthologous genes despite limited resources from related species. This is by far the first report on the breadth and completeness of transcript assemblies for coconuts. Fragments per kilobase of transcript per million mapped reads (FPKM) revealed the top twenty unigenes in each tissue. Annotated unigenes in the assemblies encode stress-response proteins like the abscisic acid-stress-ripening, auxin-repressed, heat-shock, and metallothionein-like proteins. This study not only expands the transcriptomic resources for coconuts but also provides quality sequences for functional and molecular studies geared towards molecular breeding.