Jeremiah D Hackett
Associate Department Head, Ecology and Evolutionary Biology
Associate Professor, BIO5 Institute
Associate Professor, Ecology and Evolutionary Biology
Associate Professor, Genetics - GIDP
Primary Department
Department Affiliations
(520) 621-7514
Work Summary
Jeremiah Hackett’s research interests are in the areas of genome evolution, the evolution of photosynthesis and the physiology of harmful algae. Part of his research investigates how eukaryotes acquire plastids through endosymbiosis and how this process influences genome evolution through gene transfer. Another main area of research is the ecology and physiology of harmful algae. His lab is using microarrays to determine global gene expression patterns of harmful algae under various growth conditions. These gene expression profiles will be used to determine the factors that lead to harmful algal blooms in the oceans.
Research Interest
Dr. Jeremiah Hackett, Ph.D., is Associate Professor and Department Head of Ecology and Evolutionary Biology. He received his undergraduate degree in Biology from the University of Wisconsin-Milwaukee and a Ph.D. in Genetics, University of Iowa. Dr. Hackett’s research interests are in the areas of genome evolution, evolution of photosynthesis and the physiology of harmful algae. His research investigates how eukaryotes acquire plastids through endosymbiosis and how this process influences genome evolution through gene transfer. Another main area of research is the ecology and physiology of harmful algae. Dr. Hackett uses microarrays to determine global gene expression patterns of harmful algae under various growth conditions. These gene expression profiles will be used to determine the factors that lead to harmful algal blooms in the oceans.

Publications

Yoon, H. S., Hackett, J. D., Van Dolah, F. M., Nosenko, T., Lidie, K. L., & Bhattacharya, D. (2005). Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Molecular biology and evolution, 22(5), 1299-308.

Dinoflagellates are important aquatic primary producers and cause "red tides." The most widespread plastid (photosynthetic organelle) in these algae contains the unique accessory pigment peridinin. This plastid putatively originated via a red algal secondary endosymbiosis and has some remarkable features, the most notable being a genome that is reduced to 1-3 gene minicircles with about 14 genes (out of an original 130-200) remaining in the organelle and a nuclear-encoded proteobacterial Form II Rubisco. The "missing" plastid genes are relocated to the nucleus via a massive transfer unequaled in other photosynthetic eukaryotes. The fate of these characters is unknown in a number of dinoflagellates that have replaced the peridinin plastid through tertiary endosymbiosis. We addressed this issue in the fucoxanthin dinoflagellates (e.g., Karenia brevis) that contain a captured haptophyte plastid. Our multiprotein phylogenetic analyses provide robust support for the haptophyte plastid replacement and are consistent with a red algal origin of the chromalveolate plastid. We then generated an expressed sequence tag (EST) database of 5,138 unique genes from K. brevis and searched for nuclear genes of plastid function. The EST data indicate the loss of the ancestral peridinin plastid characters in K. brevis including the transferred plastid genes and Form II Rubisco. These results underline the remarkable ability of dinoflagellates to remodel their genomes through endosymbiosis and the considerable impact of this process on cell evolution.

Soares, M. B., De, M., Hackett, J. D., & Bhattacharya, D. (2009). Expressed Sequence Tags: Normalization and subtraction of cDNA libraries. Methods in Molecular Biology, 533, 109-123.

Abstract:

Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. ESTs have also become particularly important with recent expanded efforts in complete genome sequencing of understudied, nonmodel eukaryotes such as protists and algae. For these projects, ESTs provide an invaluable source of data for gene identification and prediction of exon-intron boundaries. The generation of EST data, although straightforward in concept, requires nonetheless great care to ensure the highest efficiency and return for the investment in time and funds. To this end, key steps in the process include generation of a normalized cDNA library to facilitate a high gene discovery rate followed by serial subtraction of normalized libraries to maintain the discovery rate. Here we describe in detail, protocols for normalization and subtraction of cDNA libraries followed by an example using the toxic dinoflagellate Alexandrium tamarense. © 2009 Humana Press, a part of Springer Science+Business Media, LLC.

Moustafa, A., Evans, A. N., Kulis, D. M., Hackett, J. D., Erdner, D. L., Anderson, D. M., & Bhattacharya, D. (2010). Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PLoS ONE, 5(3).

PMID: 20300646;PMCID: PMC2837391;Abstract:

Background: Dinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions. Methodology/Principal Findings: We generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value

Herron, M. D., Hackett, J. D., Aylward, F. O., & Michod, R. E. (2009). Triassic origin and early radiation of multicellular volvocine algae. Proceedings of the National Academy of Sciences of the United States of America, 106(9), 3254-8.

Evolutionary transitions in individuality (ETIs) underlie the watershed events in the history of life on Earth, including the origins of cells, eukaryotes, plants, animals, and fungi. Each of these events constitutes an increase in the level of complexity, as groups of individuals become individuals in their own right. Among the best-studied ETIs is the origin of multicellularity in the green alga Volvox, a model system for the evolution of multicellularity and cellular differentiation. Since its divergence from unicellular ancestors, Volvox has evolved into a highly integrated multicellular organism with cellular specialization, a complex developmental program, and a high degree of coordination among cells. Remarkably, all of these changes were previously thought to have occurred in the last 50-75 million years. Here we estimate divergence times using a multigene data set with multiple fossil calibrations and use these estimates to infer the times of developmental changes relevant to the evolution of multicellularity. Our results show that Volvox diverged from unicellular ancestors at least 200 million years ago. Two key innovations resulting from an early cycle of cooperation, conflict and conflict mediation led to a rapid integration and radiation of multicellular forms in this group. This is the only ETI for which a detailed timeline has been established, but multilevel selection theory predicts that similar changes must have occurred during other ETIs.

Wisecaver, J. H., & Hackett, J. D. (2010). Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata. BMC Genomics, 11(1).

PMID: 20537123;PMCID: PMC3017763;Abstract:

Background: Dinophysis is exceptional among dinoflagellates, possessing plastids derived from cryptophyte algae. Although Dinophysis can be maintained in pure culture for several months, the genus is mixotrophic and needs to feed either to acquire plastids (a process known as kleptoplastidy) or obtain growth factors necessary for plastid maintenance. Dinophysis does not feed directly on cryptophyte algae, but rather on a ciliate (Myrionecta rubra) that has consumed the cryptophytes and retained their plastids. Despite the apparent absence of cryptophyte nuclear genes required for plastid function, Dinophysis can retain cryptophyte plastids for months without feeding.Results: To determine if this dinoflagellate has nuclear-encoded genes for plastid function, we sequenced cDNA from Dinophysis acuminata, its ciliate prey M. rubra, and the cryptophyte source of the plastid Geminigera cryophila. We identified five proteins complete with plastid-targeting peptides encoded in the nuclear genome of D. acuminata that function in photosystem stabilization and metabolite transport. Phylogenetic analyses show that the genes are derived from multiple algal sources indicating some were acquired through horizontal gene transfer.Conclusions: These findings suggest that D. acuminata has some functional control of its plastid, and may be able to extend the useful life of the plastid by replacing damaged transporters and protecting components of the photosystem from stress. However, the dearth of plastid-related genes compared to other fully phototrophic algae suggests that D. acuminata does not have the nuclear repertoire necessary to maintain the plastid permanently. © 2010 Wisecaver and Hackett; licensee BioMed Central Ltd.