Genomic Insights Into the Origin of Diatoms
Recent multi-gene phylogenetic analyses have identified several early diverging lineages in the evolution of diatoms. A small group marine unicells, the bolidophytes, represents the closest living relative of the diatoms. Comparing bolidophyte genomes to those of early diverging diatoms will allow us to pinpoint the key genomic changes that took place in the common ancestor of all diatoms. We're currently using flow cytometry to estimate the genome sizes of these species and carrying out some exploratory Illumina sequencing to characterize their organelle genomes and the repetitive fraction of their nuclear genomes.
Using Phylogeny to Understand the Evolution of Diatom Nuclear Genomes
As currently understood, the phylogeny (or "family tree") of diatoms has a number of critical unresolved branches, limiting our ability to address important unanswered questions about the evolution of this group. Two diatom genomes have been sequenced, and the genome of one species contains as many as 784 genes of recent bacterial origin, only half of which were found in the other species. This pattern points to a dynamic history of bacterial gene gain and/or loss over the course of diatom evolution. This pattern is best resolved against the backdrop of a strongly supported organismal phylogeny. We're augmenting efforts to reconstruct the diatom phylogeny and using diatom transcriptome data to disentangle the history of bacterial gene acquisitions by diatoms. Another result of this work will be the identification of ancestrally present low-copy nuclear genes that can be used to independently estimate the diatom phylogeny.
The Origins and Evolution of Diatoms in Freshwaters
Freshwater colonizations are landmark events in diatom evolution, having led to the origins of perhaps tens of thousands of species. A primary goal of this research is to understand the morphological, physiological, and genetic adaptations that have allowed diatoms to colonize and diversify in freshwater environments, which present numerous obstacles to marine colonists. We're using a blend of phylogenetic, experimental, and genomic approaches to understand how diatoms have successfully, and repeatedly, conquered what has been referred to as "the salinity barrier."
Plastid Genome Evolution in Non-photosynthetic Diatoms
Diatoms are prolific photosynthesizers, accounting for roughly one-fifth of global net primary production. An unusual set of species in the genus Nitzschia have, however, completely abandoned photosynthesis in favor of a heterotrophic lifestyle. These "apochloritic" diatoms have completely lost their ability to photosynthesize but nevertheless maintain colorless genome-bearing plastids. We are using the Illumina DNA sequencing platform to sequence total DNA from diverse photosynthetic and non-photosynthetic Nitzschia species. This approach should provide the entire nuclear ribosomal DNA array and near-complete plastid and mitochondrial genome assemblies for each species. We'll use these data to reconstruct the phylogeny of the group, allowing us to test specific hypotheses about the timing and origin of apochloritic species, e.g., how many times did heterotrophy evolve? More interesting still, the relict plastid genomes of the apochloritic species will help us identify indispensible genes in the plastid genome whose function extends beyond photosynthesis. What is the evolutionary fate of an organelle genome whose principle function has been lost? How fast do photosynthetic genes deteriorate after the shift to heterotrophy?