Research Article Open Access

Illumina-Based De Novo Transcriptome Analysis and Identifications of Genes Involved in the Monolignol Biosynthesis Pathway in Acacia koa

Kazue Ishihara1, Eric K.W. Lee1, Isabel Rushanaedy1 and Dulal Borthakur1
  • 1 University of Hawaii, United States
Current Research in Bioinformatics
Volume 4 No. 1, 2015, 7-27

DOI: https://doi.org/10.3844/ajbsp.2015.7.27

Submitted On: 9 June 2015
Published On: 6 August 2015

How to Cite: Ishihara, K., Lee, E. K., Rushanaedy, I. & Borthakur, D. (2015). Illumina-Based De Novo Transcriptome Analysis and Identifications of Genes Involved in the Monolignol Biosynthesis Pathway in Acacia koa. Current Research in Bioinformatics, 4(1), 7-27. https://doi.org/10.3844/ajbsp.2015.7.27

Abstract

Acacia koa is a leguminous timber tree endemic to the Hawaiian Islands. For breeding projects involved in improving wood quality of A. koa, understanding of genes influencing wood quality is crucial. Therefore, the objective of this study was to identify A. koa genes in the monolignol biosynthesis pathway, which is involved in wood formation and development. In this study, whole transcritpome sequencing of A. koa seedlings was performed through Illumina-based sequencing and over 88 million high-quality paired-end raw reads were generated. Trinity de novo assembly of those reads yielded 85,533 unigenes with an average length of 641 bp. Based on sequence similarity search with known proteins, we annotated 47,038 of the unigenes. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 149 unigenes were assigned to ortholog groups of enzymes involved in the monolignol biosynthesis pathway. In addition, we identified complete coding sequences of genes for all the ten identified enzymes of the pathway. Future studies on expression levels of these genes in A. koa with different wood qualities will provide a tool for selection of desirable types. Comprehensive sequence resources of A. koa generated through this study will contribute to genomic studies and improvement programs for this tree.

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Keywords

  • Acacia koa
  • Tree Legume
  • Transcriptome Analysis
  • Lignin
  • Monolignol Biosynthesis