Download Deep transcriptomics of toxic red tide dinoflagellate

Deep transcriptomics of toxic red tide dinoflagellate Alexandrium tamarense
Ahmed Moustafa1, Deana L. Erdner2, David M. Kulis3, Donald M. Anderson3, Debashish Bhattacharya1,4
1
Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA
2
Marine Science Institute, University of Texas at Austin, Port Aransas, TX
3
Woods Hole Oceanographic Institution, Woods Hole, MA
4
Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City,
IA
Dinoflagellates (Alveolata, Chromalveolata) are unicellular protists that are among the most abundant
phytoplankton in marine and freshwater ecosystems, playing a major role in primary production.
Dinoflagellates also form massive blooms that have harmful ecological and economical impacts.
Although several unique and peculiar characteristics make dinoflagellates an interesting model to extend
our understanding of the evolution of the eukaryotic cell, the footprints of endosymbiotic/horizontal gene
transfers, and the role of phytoplankton in the dynamics of the Earth’s oceans and climate, their large
genomes make them challenging models for genome-wide studies. However, recent advances in genomic
and transcriptomic methods provide novel and promising approaches to study such complex systems in a
high-throughput fashion. Here, we report the results of massively parallel signature sequencing (MPSS) to
profile global transcriptional regulation in the toxic red tide dinoflagellate Alexandrium tamarense that
was grown under four different culture conditions. Our data indicate an exceptionally high gene-content
(~40,000 unique transcripts) and complex gene-families in this unicellular species. We also provide novel
insight into differential expression patterns that reflect interactions with bacterial communities and
nutrient limitation. To the best of our knowledge, this is the first demonstration at the transcriptome level
of the switch of trophic states in Alexandrium from autotrophy to heterotrophy in the presence of bacteria.
Finally, we introduce a classification of the Alexandrium transcriptome into a major core component that
is uniformly expressed in vegetative cells regardless of environmental conditions and a minor component
that is differentially transcribed reflecting changes in cellular and environmental factors.