Teak Genome Database

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Photographer: Mr. Niti Sukumal

Teak (Tectona grandis Linn. f.) is an important tree species of the deciduous forests in South and Southeast Asia. Its natural range covers most of India, Myanmar, northern Thailand, parts of Laos and Java in Indonesia. It is a relatively fast-growing tree and has been established as a plantation species within its native range and in several other regions in the tropics. The teak wood has excellent technical properties and is highly prized for its esthetic qualities.

During the late 19^th and first half of the 20^th century teak has been logged at an unsustainable rate from the natural forests to the extent that trees of large diameter have all but disappeared. Currently logging from the natural forests is highly restricted, though illegal felling of teak trees still occurs.

To facilitate genetic improvement through breeding molecular genetic information would be very useful and therefore scientists at Center of Agricultural Biotechnology, Kasetsart University (CAB-KU) decided to sequence the genome of teak trees from Thailand. The project was funded by the Center of Excellence on Agricultural Biotechnology (AG-BIO) S&T Postgraduate Education and Research Development Office (PERDO), Commission on Higher Education (CHE), Ministry of Education. One teak tree growing on the Kasetsart University Kamphaengsaen Campus was sequenced as the reference genome and nine trees from the Royal Forest Department teak gene banks in KhonKaen and Phitsanuloke were sequenced at lower coverage to assess the genetic diversity. Using flow cytometry, the teak genome size was estimated to be about 340 Mbp. Teak has a diploid genome with 36 chromosomes.
For the reference tree, paired reads with insert size of 200 bp, 300 bp and 500 bp and mate-pairs with insert size 5 kb, and 10 kb were sequenced using Illumina Hiseq2000. After eliminating duplicates and low quality reads all remaining reads were used to build contigs and scaffolds by Plantanus version 1.2.1. The total coverage of the paired-end reads combined to about 75-80X. The genome assembly and analysis was carried out on the CAB-High Performance Computing server at CAB-KU. The annotation of the genome was done using an in house built pipeline, CABAnnot using varous open source software modules. For the nine trees from the gene bank, sequence reads were obtained from libraries with insert sizes of 200 bp and 300 bp. Polymorphisms were called by samtools after bwa-mem alignment of the reads to the reference genome.