# Genomic evolution and ecotype divergence in thraustochytrids: insights from comparative genomics and phylogenomics

## TL;DR

This study explores how thraustochytrid protists evolved into different ecotypes by comparing their genomes and identifying genetic differences linked to metabolism.

## Contribution

The study provides new molecular evidence for ecotype divergence in thraustochytrids through comparative genomics and phylogenetic analysis.

## Key findings

- Anabolic strains have larger genomes with fatty acid synthase genes, while catabolic strains have smaller genomes with hydrolytic enzyme genes.
- Phylogenetic analysis shows anabolic strains diverged recently, while catabolic strains evolved independently for over 190 million years.
- Both ecotypes have abundant fatty acid desaturase genes, with polyketide synthase genes showing ecotype-specific patterns.

## Abstract

Thraustochytrids are unicellular heterotrophic protists within the Stramenopiles group, widely distributed across marine ecosystems. Understanding the mechanisms underlying their metabolic ecotype evolution is pivotal for revealing how these organisms drive the marine carbon cycle and adapt to diverse environments.

In this study, we report a high-quality genome of Aurantiochytrium sp. TWZ-97 and conduct a comparative genomics analysis of thraustochytrid strains to investigate ecotype-specific differences in genome structure, evolutionary-developmental relationships, and core functional genes.

Comparative genomics revealed that “anabolic” strains (TWZ-97, Mn4, SW8) possess larger genomes with lower gene density, whereas “catabolic” strains (S-28, S-429) have smaller, gene-rich genomes with stable repetitive elements. Phylogenetic analyses revealed that the “anabolic” strains diverged relatively recently, around 2.389 million years ago, while the “catabolic” strains evolved independently for over 190.7 million years, reflecting prolonged, lineage-specific adaptation. Functionally, “anabolic” strains were enriched in fatty acid synthase genes, whereas hydrolytic enzyme genes were unique to the “catabolic” strains. Both ecotypes exhibited a significant abundance of fatty acid desaturase (FAD) genes, and polyketide synthase (PKS) genes displayed unique long sequences, multi-domain architectures, and ecotype-specific gene differentiation patterns.

Together, this study provides crucial molecular evidence for the genetic basis of metabolic specialization and ecotype diversification in thraustochytrids.