Jeremiah D Hackett

Jeremiah D Hackett

Associate Department Head, Ecology and Evolutionary Biology
Associate Professor, Ecology and Evolutionary Biology
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Contact
(520) 621-7514

Work Summary

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

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

Hackett, J. D., Scheetz, T. E., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L., & Bhattacharya, D. (2005). Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics, 6.

Abstract:

Background: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging. Results: Approximately 20% of the 6,723 unique (11,171 total 3′-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair. Conclusions: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production. © 2005 Hackett et al; licensee BioMed Central Ltd.

Reyes-Prieto, A., Hackett, J. D., Soares, M. B., Bonaldo, M. F., & Bhattacharya, D. (2006). Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Current biology : CB, 16(23), 2320-5.

A single cyanobacterial primary endosymbiosis that occurred approximately 1.5 billion years ago is believed to have given rise to the plastid in the common ancestor of the Plantae or Archaeplastida--the eukaryotic supergroup comprising red, green (including land plants), and glaucophyte algae. Critical to plastid establishment was the transfer of endosymbiont genes to the host nucleus (i.e., endosymbiotic gene transfer [EGT]). It has been postulated that plastid-derived EGT played a significant role in plant nuclear-genome evolution, with 18% (or 4,500) of all nuclear genes in Arabidopsis thaliana having a cyanobacterial origin with about one-half of these recruited for nonplastid functions. Here, we determine whether the level of cyanobacterial gene recruitment proposed for Arabidopsis is of the same magnitude in the algal sisters of plants by analyzing expressed-sequence tag (EST) data from the glaucophyte alga Cyanophora paradoxa. Bioinformatic analysis of 3,576 Cyanophora nuclear genes shows that 10.8% of these with significant database hits are of cyanobacterial origin and one-ninth of these have nonplastid functions. Our data indicate that unlike plants, early-diverging algal groups appear to retain a smaller number of endosymbiont genes in their nucleus, with only a minor proportion of these recruited for nonplastid functions.

Lasek-Nesselquist, E., Wisecaver, J. H., Hackett, J. D., & Johnson, M. D. (2015). Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum. BMC genomics, 16, 805.

Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system.

Molnár, I., Lopez, D., Wisecaver, J. H., Devarenne, T. P., Weiss, T. L., Pellegrini, M., & Hackett, J. D. (2012). Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). BMC Genomics, 13(1).

PMID: 23110428;PMCID: PMC3533583;Abstract:

Background: Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy.Results: A de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated.Conclusions: The construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome sequence for the Showa strain of B. braunii, race B. Further, the transcriptome database empowers future biosynthetic engineering approaches for strain improvement and the transfer of desirable traits to heterologous hosts. © 2012 Molnár et al.; licensee BioMed Central Ltd.

Hackett, J. D., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L., Scheetz, T. E., Nosenko, T., & Bhattacharya, D. (2004). Migration of the Plastid Genome to the Nucleus in a Peridinin Dinoflagellate. Current Biology, 14(3), 213-218.

PMID: 14761653;Abstract:

Dinoflagellate algae are important primary producers and of significant ecological and economic impact because of their ability to form "red tides" [1]. They are also models for evolutionary research because of an unparalleled ability to capture photosynthetic organelles (plastids) through endosymbiosis [2]. The nature and extent of the plastid genome in the dominant perdinin-containing dinoflagellates remain, however, two of the most intriguing issues in plastid evolution. The plastid genome in these taxa is reduced to single-gene minicircles [3, 4] encoding an incomplete (until now 15) set of plastid proteins. The location of the remaining photosynthetic genes is unknown. We generated a data set of 6,480 unique expressed sequence tags (ESTs) from the toxic dinoflagellate Alexandrium tamarense (for details, see the Experimental Procedures in the Supplemental Data) to find the missing plastid genes and to understand the impact of endosymbiosis on genome evolution. Here we identify 48 of the non-minicircle-encoded photosynthetic genes in the nuclear genome of A. tamarense, accounting for the majority of the photosystem. Fifteen genes that are always found on the plastid genome of other algae and plants have been transferred to the nucleus in A. tamarense. The plastid-targeted genes have red and green algal origins. These results highlight the unique position of dinoflagellates as the champions of plastid gene transfer to the nucleus among photosynthetic eukaryotes.