Charting the landscape of organellar genome evolution in eustigmatophyte algae

Area of Science:

• Genomics
• Evolutionary Biology
• Algal Biology

Background:

• Organellar genomes are crucial for understanding organismal evolution and possess biotechnological potential.
• Eustigmatophytes (eustigs) are a class of algae within the Ochrophyta phylum with limited genomic data available.
• Previous studies highlighted unique features in eustig organellar genomes, but a comprehensive analysis was lacking.

Purpose of the Study:

• To significantly expand the available organellar genome dataset for eustigmatophytes.
• To reconstruct a robust phylogeny for eustigmatophytes using organellar genomic data.
• To investigate the evolutionary dynamics and origins of unique genes within eustig organellar genomes.

Main Methods:

• Sequencing and analysis of 51 new organellar genomes from eustigmatophytes.
• Phylogenetic analyses to resolve the evolutionary relationships within eustigmatophytes.
• Comparative genomic analyses to identify gene content, gene order, and substitution rate variations.

Main Results:

• A robustly resolved eustigmatophyte phylogeny was established.
• Eustigmatophyte plastomes showed stability in gene content and order, with minor gene loss/gain.
• Eustigmatophyte mitogenomes exhibited significant variation in gene order, accessory genes, and substitution rates.
• The origins of plastid gene 'ycf95' and mitochondrial genes 'orfX' and 'orfY' were elucidated through divergence and duplication events.
• Five novel mitochondrial open reading frames (orfs) with no external homologs were identified, likely originating in the eustigmatophyte ancestor.
• Unusual tRNAs in the genus *Vischeria* were suggested to have a translation-independent function.

Conclusions:

• The expanded dataset provides a solid foundation for eustigmatophyte evolutionary studies.
• Organellar genome evolution in eustigmatophytes is characterized by plastome stability and mitogenome plasticity.
• The study clarifies the origin of previously enigmatic eustig organellar genes and identifies new mysterious mitochondrial orfs.
• Findings revise understanding of mitochondrial translation and suggest novel functions for tRNAs in specific eustigmatophyte genera.