Phylogenomic placement, description, and mitochondrial genome of a novel freshwater goniomonad (Cryptista) from Arizona: Naiadagoniomonas ponderosa n. gen. n. sp.

Background Goniomonads are heterotrophic members of a major group of eukaryotes called Cryptista and branch sister to the photosynthetic Cryptophyta. Goniomonads are poorly investigated and have recently been reclassified, dividing a single genus into ten new genera. In single-gene phylogenies, all three freshwater genera branch in a monophyletic group distinct from marine goniomonads, suggesting that a single event led to goniomonads transitioning from marine to freshwater environments. Here, we use light microscopy, scanning electron microscopy and single cell genomics to describe and determine the molecular phylogenetic placement of a new freshwater genus of goniomonad. Methods Light and scanning electron microscopy were used to validate the morphological characteristics of a new goniomonad. We used whole genome amplification to generate a goniomonad single-cell amplified genome. We reconstructed the phylogenetic placement of this goniomonad using single-gene and multi-gene analyses. Results We characterized and established a new genus of goniomonad, named Naiadagoniomonas ponderosa n. gen. n. sp. In single-gene phylogenetic analyses, N. ponderosa branches within the freshwater clade that forms the sister to Limnogoniomonas. In multi-gene phylogenetic analyses, N. ponderosa branches with the only other representative of goniomonads available. We recovered a fragmented but high-quality single-amplified genome including a complete circular-mapping mitochondrial genome. Conclusions We conclude that diverse goniomonads are likely present in freshwater environments and single-cell genomics is an excellent tool for probing their phylogenomic diversity and mitochondrial gene content.