| dc.description.abstract | Thraustochytrids are unicellular marine heterotrophs which have attention due to their ability to accumulate high amount of important nutraceuticals, in particular polyunsaturated fatty acids (PUFA). However, their biotechnological potential has not been fully utilized as the metabolism of these organisms have not been completely unraveled. One of the ways to understand metabolism of an organism to sequence and annotate its genome. Aurantiochytrium sp. T66 is one of the strains of thraustochytrids the genome of which has been sequenced and annotated previously. However, the genome assembly constructed for annotation had numerous gaps. Therefore, there was possibility that some genes might have missed the annotation process. In this study, a de novo hybrid genome assembly of Aurantiochytrium sp. T66 was constructed using MinION’s long reads and Illumina’s shotgun reads. The purpose was to build an assembly of better quality and annotate genes which might have missed the annotation process previously.
With automatic and manual functional annotation, 317 genes were identified which had not been annotated previously. PUFA synthase subunit A and C, phosphopantetheinyl transferase, and glutamine synthase are genes important for PUFA synthesis. In the previous annotation, only partial or fragmented sequences of these genes were identified. In addition to 317 genes, complete sequences of these four genes were also identified. ATP-citrate lyase, which is also an important gene for lipid synthesis and could not be detected in the published assembly of Aurantiochytrium sp. T66, could not be detected in this study either, suggesting that Aurantiochytrium sp. T66 might have some alternate gene(s) that does the task of ATP-citrate lyase, which is to prove to acetyl-CoA for lipid synthesis. Furthermore, mitochondrial genome of Aurantiochytrium sp. T66 was also identified and annotated.
The approach of constructing a hybrid assembly using MinION’s long reads and Illumina’s shotgun reads to improve the genome assembly and annotation of Aurantiochytrium sp. T66 has proven to be effective. However, there is still room for improvement of the assembly. It is suggested that further polishing the quality of the assembly might further help improve the annotation of Aurantiochytrium sp. T66. | |
