Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

Abstract

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early-diverging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.

Alexander Bowles

“…As an evolutionary plant biologist, I have enjoyed recent works on land plant evolution (de Vries & Archibald, 2018), the anatomy and evolution of lycopsid rooting structures (Hetherington & Dolan, 2016), the evolutionary success of ferns (McElwain, 2011) and discussion on the need for more nonseed plant model organisms (Rensing, 2017). Some of my favourite research papers include: studies by Xu et al (2022) and Repetti et al (2022) of the genome of Pedinomonas minor, identifying the genomic evolution of chlorophytes; analysis by Clark et al (2016) of the evolution of fern genome traits; the work by Barba-Montoya et al (2018) to constrain the timing of the diversification of angiosperms; and that of Brockington et al (2015) which found that lineage-specific radiations of key biosynthetic genes explain betalain pigmentation in the flowering plant order Caryophyllales. All of these inspiring works have helped to stimulate ideas and discussion, as well as providing excellent reviews of the literature.…”

Chromosome‐level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment

“…Over the past decade, the genomic data of several algal lineages have enabled us to gain detailed insights into their phylogeny, evolution, and adaption to changing environments (Delaroque & Boland, 2008; Worden et al ., 2009; H. Liang et al ., 2020; Li et al ., 2020; Wang et al ., 2020, 2021). A draft genome of an unidentified, marine pedinophyte was recently presented (Repetti et al ., 2022). The authors concluded that the relatively small genome of 27.9 Mb indicated positive selection for genome streamlining in this organism, independent of other Chlorophyta.…”