Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

• DOI: 10.1186/s12864-018-4904-6
• Publication Date: 2018-07-17T12:01:09Z
• Authors: Zhiquan Song; Jason E. Stajich; Yunxuan Xie; Xianhua Liu; Yaodong He; Jinfeng Chen; Glenn R. Hicks; Guangyi Wang
• Keywords: 570; Biomedical and clinical sciences; Docosahexaenoic Acids; Bioinformatics; Bioinformatics and Computational Biology; Ecological and Environmental Phenomena; QH426-470; Microbiology; Medical and Health Sciences; Industrial Biotechnology; 03 medical and health sciences; Information and Computing Sciences; Complementary and Integrative Health; Genetics; 2.2 Factors relating to the physical environment; 14. Life underwater; Life Below Water; Phylogeny; Nutrition; Unsaturated; 0303 health sciences; Genome; Thraustochytrids; Comparative genomics; Fatty Acids; Molecular Sequence Annotation; Genomics; Biological Sciences; Ecological function; Biosynthetic Pathways; Biological sciences; Gene Ontology; Whole genome sequencing; Multigene Family; Dietary Supplements; Fatty Acids, Unsaturated; Polyunsaturated fatty acids; TP248.13-248.65; Stramenopiles; Biotechnology; Research Article

Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in environments. They well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (ω-3-PUFAs) (e.g., docosahexaenoic acid (DHA)) and hydrolytic enzymes. Thraustochytrid biomass has been estimated surpass that of bacterioplankton both coastal oceanic waters indicating they have an important role microbial food-web. Nevertheless, the molecular pathway regulatory network PUFAs production mechanisms underlying ecological functions thraustochytrids remain largely unknown. The genomes two strains (Mn4 SW8) DHA were sequenced assembled a hybrid sequencing approach utilizing Illumina short paired-end reads Pacific Biosciences long generate highly accurate genome assembly. Phylogenomic comparative genomic analyses found DHA-producing thraustochytrid similar possessed gene content. Analysis conventional synthesis (FAS) polyketide synthase (PKS) systems only detected incomplete fragmentary pathways these strains. Surprisingly, secreted carbohydrate active enzymes (CAZymes) be significantly depleted 2 as compared other relatives. Furthermore, possess expanded repertoire signal transduction self-propelled movement, which could adaptations dynamic Our results demonstrate possibility third besides previously described FAS PKS encoded Moreover, lack complete set enzymatic machinery degrading plant-derived organic materials suggests play nutritional source rather than nutrient-producer microbial-food web. Results this study suggest types saprobic world's ocean. first group, does not cellulosic live 'left-over' scavenger bacterioplankton, serves dietary plankton higher trophic levels possesses capacity on detrital matters ecosystems.