My research focuses on understanding how plants adapt to environmental challenges. I use tools of molecular biology and comparative genomics, on Arabidopsis-related extremophytes, Schrenkiella parvula and Eutrema salsugineum. S. parvula is native to the shores of a hypersaline lake, Tuz Gölü in Turkey, where the lake water contains a salt concentration up to six times higher than seawater. Mirroring its natural habitat, S. parvula is tolerant to high concentrations of multiple ions toxic to most plants. E. salsugineum, another halophyte found in arid lands of northern China, Canada and Russia, shows resistance to salt stress and freezing.
While working as a visiting scholar/postdoctoral researcher at the University of Illinois at Urbana-Champaign and the Purdue University, I contributed to advancing our understanding of plant stress adaptation mechanisms using these species as models. In 2005, I started developing RNAi-transgenic plants to explore the functions of E. salsugineum orthologs of salt stress-related SOS1 and HKT1. The results signified the first successful application of the RNAi technique on the species as well as confirmation of hypotheses generated by comparison of model and its extremophyte relatives using transgenic plants.
Since 2009, with the advent of “Next-generation sequencing (NGS)” technologies, I played a leading role in sequencing, annotating, and analyzing the genomes of S. parvula and E. salsugineum (formerly Thellungiella parvula and Thellungiella salsuginea). These works proved that NGS technology can be successful in assembling high-quality genomes of non-model plant species. The two extremophyte species, in addition to the model plant Arabidopsis, provided an excellent comparative framework in exploring the radiation of closely-related species adapting to different environments.
After I joined the LSU in 2013, I continued to study the mechanisms of adaptive evolution using the comparative genomics framework. I developed methods to systematically analyze results of inter-species comparative RNAseq, identifying co-regulated modules of orthologous gene pair/groups in multiple closely-related species. By comparing the gene expression profiles between S. parvula and Arabidopsis, I identified gene order rearrangement events, including tandem gene duplication and gene transposition, that lead to divergence in regulatory sequences and basal-level gene expression strengths.
On-going works include: (1) developing bioinformatics tools to facilitate comparative genomics analyses, especially detecting co-linearity and erosion of it through gene duplication and transposition among multiple closely related genomes, (2) identifying ortholog modules and gene regulatory networks responding differently to multi-ion salt stresses among S. parvula, E. salsugineum, and Arabidopsis, (3) incorporating regulatory sequence elements (e.g. promoters and enhancers) into the comparative genomic framework, (4) testing hypotheses generated by comparative studies using transgenic plants and the CRISPR/Cas9 system, and (5) improving genome annotations and developing novel functional genomics tools for the extremophyte species.
I am also continuing analyses on genomes and transcriptomes of various plants and non-plant organisms in collaborations with other groups, based on my NGS-related and bioinformatics expertise. On-going collaboration and consultation include those with Drs. Aaron Smith, John Larkin, and Craig Hart in the Department of Biological Sciences, LSU, Dr David Mendoza Cozatl (UMO), Dr. Tai-Ping Sun (Duke), Dr. José Dinneny (Carnegie Institute), and international collaborations with Drs. Bronwyn Barkla (UNAM, Mexico), Dae-Jin Yun (GNU, South Korea), and Sunghoon Lee (TeraBIO, South Korea).
