Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

Area of Science:

• Phycology
• Evolutionary Biology
• Genomics

Background:

• Green algae (Chlorophyta) are crucial photosynthetic eukaryotes with incompletely understood evolutionary histories.
• The Trebouxiophyceae class exhibits significant ecological diversity, including symbiotic and free-living forms across varied habitats.
• Morphological similarities among species hinder accurate diversity assessment and evolutionary analysis.

Purpose of the Study:

• To resolve the evolutionary relationships among major lineages within the Trebouxiophyceae.
• To establish a robust phylogenetic framework for understanding Trebouxiophyceae evolution.
• To utilize a chloroplast phylogenomic approach for phylogenetic reconstruction.

Main Methods:

• Sequencing of 29 chlorophyte chloroplast genomes.
• Assembly of amino acid and nucleotide datasets from 79 chloroplast genes across 61 chlorophytes.
• Phylogenetic inference using maximum likelihood and Bayesian methods with various sequence evolution models.

Main Results:

• Phylogenetic analyses consistently identified two primary Trebouxiophyceae groups: core trebouxiophyceans and a basal divergence with Chlorellales and Pedinophyceae.
• Core trebouxiophyceans form a grade sister to Chlorophyceae + Ulvophyceae, including a novel lineage (Pleurastrosarcina brevispinosa).
• Early-diverging core trebouxiophyceans are predominantly planktonic, while derived lineages comprise terrestrial/aeroterrestrial species.

Conclusions:

• The Trebouxiophyceae class is not monophyletic, necessitating a re-evaluation of its classification.
• The study provides a robust phylogeny, offering insights into the class's internal structure and evolutionary trajectory.
• New understanding of lifestyle adaptations, from aquatic to terrestrial environments, is presented.