Current Research in Bioinformatics

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

Kazue Ishihara, Eric K.W. Lee, Isabel Rushanaedy and Dulal Borthakur

DOI : 10.3844/ajbsp.2015.7.27

Current Research in Bioinformatics

Volume 4, Issue 1

Pages 7-27


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.


© 2015 Kazue Ishihara, Eric K.W. Lee, Isabel Rushanaedy and Dulal Borthakur. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.