Evolutionary genomics and phylogenomics
at
University of Arkansas

Diatoms are one of the most species-rich and diverse lineages of microbial eukaryotes. The order Thalassiosirales represents an abundant and widespread lineage of centric diatoms that have made the transition from marine to freshwater habitats multiple times. To understand the genomic and genetic processes involved in the marine to freshwater transition and adaptation, I have sequenced complete genomes and transcriptomes from across the order. We will use these resources in multiple ways, including:

• the estimation of phylogenomic relationships and the number of marine-freshwater transitions (Roberts et al. 2023),
• the evolution of genome size and its impacts on diatom ecology (Roberts et al. 2024),
• the evolutionary dynamics of repetitive elements, and
• the impacts of genome duplication and gene family evolution on silica transport genes (Bryłka et al. 2023).

We have already released an updated version of the Cyclotella cryptica genome assembled using Oxford Nanopore long reads (Roberts et al. 2020) and will be releasing additional reference-quality Thalassiosirales genomes (Roberts et al. 2025).

Other ongoing collaborative projects are investigating several evolutionary and ecological questions, including:

• the species delimitation of a cosmopolitan marine diatom using both genome resequencing and global metabarcoding datasets,
• the assembly of over 60 new chloroplast and mitochondrial genomes from the Thalassiosirales to explore evolutionary dynamics in these organelles,
• the evolution of gene expression in a set of freshwater generalist and specialist diatoms to identify genetic pathways important for freshwater adaptation, and
• myDiatoms, a citizen science project that aims to introduce students, naturalists, and the public to diatoms and help us document biodiversity across all aquatic habitats.

While diatoms are predominantly photosynthetic, there are examples of species where photosynthesis has been lost. We sequenced and annotated the first genome of a nonphotosynthetic diatom (Nitzschia sp. Nitz4; Onyshchenko et al. 2021). We found the loss of photosynthesis-related genes, evidence for the remodeling of mitochondrial glycolysis to maximize ATP yield, and evidence for the presence of a β-ketoadipate pathway.

This work formed the basis of my doctoral dissertation. Achimenes is a small genus of 26 species native to Mexico and Central America that contains enormous variation in floral form that is closely tied to pollinator preferences. I sequenced, assembled, and annotated the floral transcriptomes for 10 species of Achimenes. I used phylogenomic methods to estimate species relationships and found evidence for introgression between species pairs with similar floral form and pollination syndromes (Roberts and Roalson 2018). I also performed comparative analyses of gene expression and co-expression during flower development across the same species to identify pathways and genes relevant for flower diversification (Roberts and Roalson 2017, Roberts and Roalson 2020).

The Gesneriaceae (African violet family) represents a large lineage (>3500 species) with an enormous amount of diversity, particularly in floral form and growth form. The family is known for its diverse flowers that are visited by a number of different pollinators, as well as containing a high number of epiphytes, lithophytes, and unifoliate plants. We constructed a dated phylogeny of 768 species and found evidence for the impacts of geography, hummingbird pollination, and epiphytism influencing diversification rates in neotropical and paleotropical Gesneriaceae (Roalson and Roberts 2016).