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Transcriptome reveals senescing callus tissue of Aquilaria malaccensis, an endangered tropical tree, triggers similar response as wounding with respect to terpenoid biosynthesis

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Abstract

Aquilaria malaccensis is an endangered tree species listed in the Appendix II of CITES. It is a main source of highly valuable resinous wood known as agarwood, which is rich in secondary metabolites. De novo assembly of sequences produced by transcriptome sequencing using next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms such as Aquilaria. To investigate the genes and pathways that might control molecular mechanism of A. malaccensis under controlled environment, we sequenced two transcriptome libraries constructed from mRNAs of healthy and senescing callus tissues using Illumina sequencing. We obtained 200,062,275 and 166,544,202 reads for healthy and senescing callus libraries, respectively. We compiled 231,594 transcripts and identified 107,593 transcripts by similarity analysis against the National Center for Biotechnology Information (NCBI) public database. A total of 96,743 transcripts were functionally annotated using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. We assigned 46,076 of the transcripts to a total of 144 KEGG pathways. We focused on genes identified as contributing to fragrant compound synthesis and defense response pathways, which are important pathways leading to agarwood compound formation. This study provides abundant transcriptomic data and valuable sequence resources for future genomic studies on A. malaccensis. This is the first report of callus transcriptome from A. malaccensis.

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Acknowledgments

The authors wish to acknowledge the Malaysia Genome Institute (Microarray) for providing the Bioanalyzer service and Prof. Chuck Cannon of Xishuangbanna Tropical Botanical Garden, China, for hosting a research attachment. A deep appreciation is also given to Zhang Di and Kwong Qi Bin for their bioinformatics advices and guidance and to two anonymous reviewers for their constructive comments. This project was supported by the Universiti Putra Malaysia Research University Grant Scheme (Project Nos. 03-01-09-0829RU and 03-02-11-1369RU).

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Authors and Affiliations

  1. Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

    Chai Har Siah & Rozi Mohamed

  2. Department of Molecular and Cell Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

    Parameswari Namasivayam

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  1. Chai Har Siah
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  2. Parameswari Namasivayam
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  3. Rozi Mohamed
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Correspondence to Rozi Mohamed.

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The authors declare that they have no conflict of interest.

Data Archiving Statement

Sequencing data are available through DDBJ DRA004069, BioProject PRJDB4215. They include 75-bp paired-end reads in BAM format for two samples that were run on an Illumina Hiseq2000 at the Michael Smith Genome Science Center, Canada, on April 2012. The samples were senescing (SAMD00040776) and healthy (SAMD00040775) calli growing on the same medium, collected after 35 and 20 days, respectively.

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Communicated by W. Ratnam

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Siah, C.H., Namasivayam, P. & Mohamed, R. Transcriptome reveals senescing callus tissue of Aquilaria malaccensis, an endangered tropical tree, triggers similar response as wounding with respect to terpenoid biosynthesis. Tree Genetics & Genomes 12, 33 (2016). https://doi.org/10.1007/s11295-016-0993-z

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