Perna, N. T., III, G. P., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., Posfai, G., Hackett, J., Klink, S., Boutin, A., Shao, Y., Miller, L., Grotheck, E. J., Davis, N. W., Lim, A., , Dimalanta, E. T., et al. (2001). Erratum: Genome sequence of enterohaemorrhagic Escherichia coli 0157:H7 (Nature (2001) 409 (529-533)). Nature, 410(6825), 240-.
Wisecaver, J. H., & Hackett, J. D. (2011). Dinoflagellate genome evolution. Annual review of microbiology, 65, 369-87.
The dinoflagellates are an ecologically important group of microbial eukaryotes that have evolved many novel genomic characteristics. They possess some of the largest nuclear genomes among eukaryotes arranged on permanently condensed liquid-crystalline chromosomes. Recent advances have revealed the presence of genes arranged in tandem arrays, trans-splicing of messenger RNAs, and a reduced role for transcriptional regulation compared to other eukaryotes. In contrast, the mitochondrial and plastid genomes have the smallest gene content among functional eukaryotic organelles. Dinoflagellate biology and genome evolution have been dramatically influenced by lateral transfer of individual genes and large-scale transfer of genes through endosymbiosis. Next-generation sequencing technologies have only recently made genome-scale analyses of these organisms possible, and these new methods are helping researchers better understand the biology and evolution of this enigmatic group of eukaryotes.
Hackett, J. D., Maranda, L., Yoon, H. S., & Bhattacharya, D. (2003). Phylogenetic evidence for the cryptophyte origin of the plastid of Dinophysis (Dinophysiales, Dinophyceae). Journal of Phycology, 39(2), 440-448.
Abstract:
Photosynthetic members of the genus Dinophysis Ehrenberg contain a plastid of uncertain origin. Ultrastructure and pigment analyses suggest that the two-membrane-bound plastid of Dinophysis spp. has been acquired through endosymbiosis from a cryptophyte. However, these organisms do not survive in culture, raising the possibility that Dinophysis spp. have a transient kleptoplast. To test the origin and permanence of the plastid of Dinophysis, we sequenced plastid-encoded psbA and small subunit rDNA from single-cell isolates of D. acuminata Claparède et Lachman, D. acuta Ehrenberg, and D. norvegica Claparède et Lachman. Phylogenetic analyses confirm the cryptophyte origin of the plastid. Plastid sequences from different populations isolated at different times are monophyletic with robust support and show limited polymorphism. DNA sequencing also revealed plastid sequences of florideophyte origin, indicating that Dinophysis may be feeding on red algae.
Hackett, J. D., Wisecaver, J. H., Brosnahan, M. L., Kulis, D. M., Anderson, D. M., Bhattacharya, D., Plumley, F. G., & Erdner, D. L. (2013). Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates. Molecular biology and evolution, 30(1), 70-8.
Dinoflagellates produce a variety of toxic secondary metabolites that have a significant impact on marine ecosystems and fisheries. Saxitoxin (STX), the cause of paralytic shellfish poisoning, is produced by three marine dinoflagellate genera and is also made by some freshwater cyanobacteria. Genes involved in STX synthesis have been identified in cyanobacteria but are yet to be reported in the massive genomes of dinoflagellates. We have assembled comprehensive transcriptome data sets for several STX-producing dinoflagellates and a related non-toxic species and have identified 265 putative homologs of 13 cyanobacterial STX synthesis genes, including all of the genes directly involved in toxin synthesis. Putative homologs of four proteins group closely in phylogenies with cyanobacteria and are likely the functional homologs of sxtA, sxtG, and sxtB in dinoflagellates. However, the phylogenies do not support the transfer of these genes directly between toxic cyanobacteria and dinoflagellates. SxtA is split into two proteins in the dinoflagellates corresponding to the N-terminal portion containing the methyltransferase and acyl carrier protein domains and a C-terminal portion with the aminotransferase domain. Homologs of sxtB and N-terminal sxtA are present in non-toxic strains, suggesting their functions may not be limited to saxitoxin production. Only homologs of the C-terminus of sxtA and sxtG were found exclusively in toxic strains. A more thorough survey of STX+ dinoflagellates will be needed to determine if these two genes may be specific to SXT production in dinoflagellates. The A. tamarense transcriptome does not contain homologs for the remaining STX genes. Nevertheless, we identified candidate genes with similar predicted biochemical activities that account for the missing functions. These results suggest that the STX synthesis pathway was likely assembled independently in the distantly related cyanobacteria and dinoflagellates, although using some evolutionarily related proteins. The biological role of STX is not well understood in either cyanobacteria or dinoflagellates. However, STX production in these two ecologically distinct groups of organisms suggests that this toxin confers a benefit to producers that we do not yet fully understand.
Lim, A., Dimalanta, E. T., Potamousis, K. D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., Perna, N. T., Plunkett, G., Burland, V., Mau, B., Hackett, J., Blattner, F. R., Anantharaman, T. S., Mishra, B., & Schwartz, D. C. (2001). Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome research, 11(9), 1584-93.
We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.
