Wen Yingying, Zhu Xingyu, Li Jiaqian, Liu Xiuping, Li Qixuan, Wang Guangyi
Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China.
Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.
Front Microbiol. 2025 Jun 30;16:1608951. doi: 10.3389/fmicb.2025.1608951. eCollection 2025.
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 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.
破囊壶菌是不等鞭毛类中的单细胞异养原生生物，广泛分布于海洋生态系统中。了解其代谢生态型进化的潜在机制对于揭示这些生物如何驱动海洋碳循环以及适应不同环境至关重要。
在本研究中，我们报道了 sp. TWZ - 97 的高质量基因组，并对破囊壶菌菌株进行了比较基因组学分析，以研究基因组结构、进化发育关系和核心功能基因的生态型特异性差异。
比较基因组学表明，“合成代谢”菌株（TWZ - 97、Mn4、SW8）具有较大的基因组，基因密度较低，而“分解代谢”菌株（S - 28、S - 429）具有较小的、富含基因的基因组，其重复元件稳定。系统发育分析表明，“合成代谢”菌株在相对较近的时间分化，大约在238.9万年前，而“分解代谢”菌株独立进化超过1.907亿年，反映了长期的、谱系特异性的适应。在功能上，“合成代谢”菌株富含脂肪酸合酶基因，而水解酶基因是“分解代谢”菌株所特有的。两种生态型都表现出大量的脂肪酸去饱和酶（FAD）基因，聚酮合酶（PKS）基因具有独特的长序列、多结构域结构和生态型特异性基因分化模式。
总之，本研究为破囊壶菌代谢特化和生态型多样化的遗传基础提供了关键的分子证据。
