Chromosome-level genome of Pedinomonas minor project

The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the “core chlorophytes”. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. Although the genome is relatively small (55 Mb), it shares many traits with those of core chlorophytes including number of introns, mRNA lengths, number of protein-coding genes and abundance of repetitive elements. P. minor is a “naked” flagellate, only bound by the plasma membrane, thriving in temporary habitats such as small puddles that frequently dry-out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Phylogenomic analyses indicated that horizontal gene transfers from fungi and bacteria contributed to the evolution of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome.