Our research on phytoplankton is fairly diverse in nature but currently focuses on dinoflagellates, a phylum closely related to malaria parasite, apicomplexans, and ciliates. Dinoflagellates are important primary producers. Many of them are heterotrophic or mixotrophic. Symbiodinium (zooxanthellae) is essential to growth of reef-building corals. Dinoflagellates are major contributors of red tides (or harmful algal blooms), and some of them produce toxins. We are interested in how these organisms came to be what they are and do what they do, from a genomic perspective. Their genome is enormous, and their gene expression pattern and regulation are unusual compared to other eukaryotes. We study genome makeup, evolution, transcriptome, mRNA editing, and molecular markers (for phylogeny, population dynamics, and in situ cell division rate).
Hou, Y. and Lin, S. 2009. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes. PLoS ONE 4(9): e6978. doi 10.1371/journal.pone.0006978.
Zhang, H., Campbell, D. A., Strum, N. R. and Lin, S. 2009. Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. Mol. Biol. Evol. 26: 1757-1771.
Lin, S., Zhang, H., Hou, Y., Zhuang, Y. and Miranda, L. 2009. High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob for dinoflagellate DNA barcoding. Appl. Environ. Microbiol. 75: 1279-1290.
Lin, S., Sandh, G., Zhang, H., Cheng, J., Perkins, K., Carpenter, E. J. and Bergman, B. 2009. Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyceae): remarkable sequence divergence and possible functional diversification. J. Exp. Mar. Biol. Ecol. 371: 93-101.
Lin, S., Zhang, H. and Gray, M. W. 2008. RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In: H. Smith (ed.), RNA and DNA editing: Molecular Mechanisms and Their Integration into Biological Systems. John Wiley & Sons, Inc. p280-309.
Zhang, H., Litaker, W., Vandersea, M. W., Tester, P. and Lin, S. 2008. Geographic distribution of Karlodinium veneficum in the US east coast as detected by dual-gene Real-Time PCR assay. J. Plankton Res. 30: 905-922.
Zhang, H., Hou, Y., Miranda, L., Campbell, D. A., Sturm, N. R., Gaasterland, T. and Lin, S. 2007. Spliced leader RNA trans-splicing in dinoflagellates. Proc. Natl. Acad. Sci. USA 104: 4618-4623.
