Data Sheet 1_Genomic evolution and ecotype divergence in thraustochytrids: insights from comparative genomics and phylogenomics.docx

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

背景 破囊壶菌（Thraustochytrids）是隶属于不等鞭毛类（Stramenopiles）的单细胞异养原生生物，广泛分布于各类海洋生态系统中。解析其代谢生态型演化的内在机制，对于阐明这类生物如何驱动海洋碳循环并适应多样环境具有关键意义。
方法 本研究报道了金黄藻虫属（Aurantiochytrium）菌株TWZ-97的高质量基因组，并对多株破囊壶菌菌株开展比较基因组学分析，以探究不同生态型菌株在基因组结构、演化发育关系以及核心功能基因上的特异性差异。
结果 比较基因组学分析显示，“合成型”（anabolic）菌株（TWZ-97、Mn4、SW8）拥有更大的基因组且基因密度更低；而“分解型”（catabolic）菌株（S-28、S-429）的基因组更小且基因富集度更高，重复元件更稳定。系统发育分析表明，“合成型”菌株的分化时间相对较近，约为238.9万年前；而“分解型”菌株的独立演化时长已超过1.907亿年，这反映了长期的谱系特异性适应。功能层面，“合成型”菌株富含脂肪酸合酶基因，而水解酶基因为“分解型”菌株所特有。两类生态型菌株均显著富集脂肪酸去饱和酶（fatty acid desaturase, FAD）基因，聚酮合酶（polyketide synthase, PKS）基因则展现出独特的长序列特征、多域结构以及生态型特异性的基因分化模式。
结论 综上，本研究为破囊壶菌的代谢特化与生态型分化的遗传基础提供了关键的分子证据。