Genome Technology Research Unit focuses on addressingbiological questions through advanced post-genomics and functional genomic platform technology, namely, next generation sequencing (NGS), high-throughput proteomics, bioinformatics, high performance computing, and applications of geographic informatics technology. These platforms combining with plant cell culture are mainly used for plant research, which is also the main focus of the Unit.
- Genomic Research. The focus is in the area of structural, evolutionary and functional genomics of microbes, plants and animals. Research on microbial genomes includes Spirulina, insect-fungi, yeasts, metagenome sequencing and detection of variation in viral genomes. We also employ genomic technologies, such as RNA-sequencing, genotyping by sequencing, targeted enrichment sequencing, construction of BAC/fosmid libraries, to study complex eukaryotic organisms such as oil palm (Elaeis spp.), rubber tree (Hevea brasiliensis), cassava (Manihot esculenta), mungbean (Vigna radiata), maize, eucalyptus and black tiger shrimp (Penaeus monodon).
- Proteomics Research. The focus is on various fields of High-throughput proteomics technology, including 2D-PAGE, shotgun proteomics or GeLC-MS, MALDI-TOF protein profile, MALDI-biotyper, protein-protein interaction, phosphoproteomics and glycoproteomics. Examples of studies include proteins related with ovarian development in the black tiger shrimp, cancer biomarker discovery and high-throughput detection of bioactive peptides.
- Bioinformatics Research. The main aim is to establish sustainable computational platform technology for extracting biological information and providing potential hypotheses to research problems. Bioinformatic research efforts largely utilize multidisciplinary skills, e.g. computer science, statistics, chemistry, and biology. The scopes include (i) construction of genomic databases (ii) bioinformatics algorithm development (iii) data-mining of large-scale genomic information (iv) medical informatics and (v) functional studies using in silico methodologies.
- Plant Research focusing on development of plants tolerant to drought and soil salinity, understanding of starch biosynthesis and storage organ development at the molecular level in tuber crops, gene transformation to increase the quality of economic crops and understanding of genes function in rice to facilitate rice breeding, as well as model development and applications of high quality spatial databases for land resources management, ecosystem, environment and monitoring by employing Geographic Information System (GIS), Global Positioning System (GPS) and Satellite Remote Sensing (SRS).
List of Laboratories
- Genomic Research Laboratory
- Proteomics Research Laboratory
- Biostatistics and Bioinformatics Laboratory
- Plant Research Laboratory
- Plant Molecular Genetics and Biotechnology Laboratory
- Plant Physiology and Biochemistry Laboratory
- Geoinformatics Laboratory
- DNA markers associated with agronomical traits in cassava, rubber tree, rice, maize, sorghum, cucumber, etc.
- Genomic tools: DNA sequencing and genotyping.
- EST databases: rubber tree and oil palm.
- Human variation databases: Pan-Asian SNP, Thai SNP, Thailand human mutation and variation.
- Primer designing tools: WASP, RExprimer.
- Bioinformatic hardware accelerated tools, e.g., field programmable gate array (FPGA) and graphic processing unit (GPU).
- A novel clustering tool, called iterative principal component analysis (ipPCA), for population genomics analysis.
- Salt-tolerant varieties of tropical plants such as rice, sugarcane, eucalyptus screened under controlled environment in vitro culture.
- Transformation systems for tomato, cassava, potato, orchid and ornamental gingers.
- Molecular characterization of plant viruses infecting cucurbits, pepper and tomato.
- Expression of plant viral gene in E. coli system for production of polyclonal antibody and monoclonal antibodies.
- Identification of potential promoter for control of expression in plant.
- Characterization of genes participating in sucrose partitioning and starch biosynthesis pathways in cassava.
- Identification and molecular characterization of genes involved in storage root formation and development in cassava.
- Somatic embryogenesis and regeneration & protoplast technology in recalcitrant ornamental gingers.
- Functional characterization of cassava genes and proteins using E. coli, yeast and model plants (Arabidopsis thaliana and potato).
- Detection and mapping of salt affected soils in Northeastern Thailand.
- Model development for increasing sugarcane management by using geographic informatics technology.
- Detection of hardpan and spectral reflectance of cassava plantation under water stresses.
Major Equipment and Facilities
- Sequencing facility: The next generation Genome Sequencer (GS) FLX, Ion Torrent Sequencer, and Pacific Biosciences RSII
- Proteomics facility: 2D-gel electrophoresis, Image analysis software, nano LC-MS/MS, MALDI-TOF/TOF MS
- High Performance computing systems:
- 22-node SUN microsystem cluster computer connected via 20Gbps infiniband network switch. Each node contains 32 computational cores of AMD 2.3 GHz with 64GB of memory (except one node with 172 GB of memory). The parallel file system of 10 TB administrated by Lustre is attached to the system providing enough space for the most intensive tasks.
- Apple G5 cluster with 46 computational nodes. Each node contains two G5 64-bit vector processors connected via a 10Gbps Ethernet switch.
- All genomic databases and all in-house web-based bioinformatic tools are operated by a separate database SUN microsystem server containing 12 AMD cores at 2.3GHz with 64GB or RAM.
- Plant genetic engineering facilities:
- High-pressure gene gun and greenhouses for transgenic plant biosafety evaluation
- Tissue culture facilities for plant transformation
- Geographic informatics equipments including: RS & GIS software, GPS, Field Spectrometer, SPAD, and LAI
Dr. Sithichoke Tangphatsornruang
113 Thailand Science Park
Phahonyothin Road, Khlong Nueng, Khlong Luang
Pathum Thani 12120, Thailand
Tel: +66 (0) 2564 6700
Fax: +66 (0) 2564 6584