Area of Interest

In my lab, we seek to characterize and compare genomes to better understand genetic and evolutionary processes linking genotypes to phenotypes.  A central feature of this is sequencing and decoding plant genomes. The overarching goal of my research is to understand how to interpret complex and fascinating messages embedded in genomes.

Why do we need to decode new genomes? Using genetic diversity to explain phenotypic diversity is necessary to understand life. Novel genomes allow novel ways of discovering and interpreting the genetic mechanisms underlying physiological and evolutionary processes. Insight gained from such processes will be needed in the development of crops for sustainable agriculture and effective conservation strategies, especially in the face of climate change, overpopulation, and increasing demand for food and bioenergy crops.  For example, genomes from wild relatives of crop species can reveal unique genetic features that can be harnessed to improve the crops through breeding.  This can be a highly desirable alternative to genetic engineering.  Efforts in plant breeding are as old as the domestication of crops themselves, but further enhancement requires the exploitation of novel genetic resources.

How do we decode a new genome? Next Generation Sequencing technologies have revolutionized the field of genomics, providing new platforms applicable to any organism. However, understanding the blueprint of genomes continues to be a complex challenge. For example, being sessile, plants survive by adapting to changing environments. In adapting to environmental stress, evolutionary solutions have been achieved over time scales of millions of years, virtually in all plants, and for different stress types and severity. Some plants have evolved to be experts in adapting to extreme environmental conditions. These plants, called extremophiles should reflect the evolutionary trajectory leading to these capacities. By using both well studied models and new genomes, we can explore what the genome-level differences mean and how they translate into distinct phenotypes and lifestyles.

 

Selected Publications

H. Wu*, Z. Zhang*, J. Wang*, D. Oh*, M. Dassanayake*, B. Liu*, Q. Huang*, H. Sun, R. Xia, Y. Wu,
Y. Wang, Z. Yang, Y. Liu, W. Zhang, H. Zhang, J. Chu, C. Yan, S. Fang, J. Zhang, Y. Wang, F. Zhan, G. Wang, S. Lee, J. Cheeseman, B. Yang,B. Li, J. Min, L. Yang, J. Wang, C. Chu, S. Chen, H. Bohnert, J. Zhu, X. Wang, Q. Xie, (2012), Gene Complement and Small RNA Complexity Support the Abiotic Stress Tolerance Phenotype of Thellungiella salsuginea – a Genome-based View. Proceedings of the National Academy of Sciences, 109(30), pp12219-24.

D. Oh*, M. Dassanayake*, H. J. Bohnert, and J. M. Cheeseman. (2012) Life in the extreme: Lessons from the Genome. Genome Biology, 13(3), pp241-249.

M. Dassanayake*, D. Oh*, J. Haas, A. Hernandez, H. Hong, S. Ali, D. Yun, R. Bressan, J. Zhu, J. M. Cheeseman, and H. J. Bohnert. (2011), The Genome of an extremophile Arabidopsis-relative: Thellungiella parvula. Nature Genetics, 43, pp913–918.

M. Dassanayake, D. Oh, D. Yun, R. Bressan, J. M. Cheeseman, H. J. Bohnert. (2011) “The Scope of Things to come - new Paradigms in Biotechnology” in: Plant Biotechnology and Agriculture: Prospects for the 21st Century, eds. A. Altman and M. Hasegawa, Elsevier. ISBN: 978-0-12-381466-1.

M. Dassanayake, D. Oh, H. Hong, H. J. Bohnert, and J. M. Cheeseman (2011), Transcription strength and halophytic lifestyle, Trends in plant science, 16(1), pp1-3.

Dong-Ha Oh*, Maheshi Dassanayake*, J. Haas, A. Kropornika, C. Wright, M. Urzo, H. Hong, S. Ali, A. Hernandez, G. Lambert, G. Inan, D. Galbraith, R. Bressan, D. Yun, J. Zhu, J. Cheeseman, H. Bohnert. (2010), Genome Structures and Halophyte-Specific Gene Expression of the Extremophile Thellungiella parvula in Comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis, Plant Physiology, 154, pp1040-1052.

M. Dassanayake, J. Haas, H. J. Bohnert, J. M. Cheeseman (2010), Comparative Transcriptomics for Mangrove Species: An Expanding Resource, Functional and Integrative Genomics, 10(4), pp523-32.

M. Dassanayake, J. Haas, H. J. Bohnert, J. M. Cheeseman (2009), Shedding Light on an Extremophile Lifestyle through Transcriptomics, New Phytologist, 183(3), pp764-775.

* contributed equally to this work

 

I invite postdoctoral researchers, graduate, and undergraduate students with an interest in plant evolution and comparative genomics to contact me. Experience in programing will be desirable, but a curiosity in biology of evolutionary adaptations and enthusiasm to learn new computational methods will be essential.