Presentation Information
[P03-319]Telomere-to-Telomere Genome Assembly and Annotation of Rhodotorula toruloides NP11
○ziyan Wang1, Zongbao Kent Zhao1 (1. Dalian University of Technology (China))
Keywords:
Rhodotorula toruloides,Genome Assembly,Genome Annotation
Rhodotorula toruloides is an oleaginous yeast of basidiomycota with considerable potential in biorefinery applications. However, its genetic basis and functional diversity remain poorly understood due to insufficient genome assembly and annotation. In this study, we performed a genome reassembly and refinement of the R. toruloides NP11 using multi-platform sequencing data, leading to telomere-to-telomere assembly with significantly improved genome continuity, completeness, and structural accuracy. Telomeric regions and repetitive sequences were systematically characterized, revealing key features of genome organization and structure and providing base for future evolutionary and functional studies.
For functional annotation, we established a multi-layered annotation framework integrating homology-based prediction, InterProScan domain identification, and protein structure-based functional inference using AlphaFold3. This approach enabled comprehensive annotation and classification of protein-coding genes across the genome. Notably, proteins that are difficult to characterize using conventional methods were properly annotated. Furthermore, comparative genomic analysis of NP11 with other R. toruloides strains indicated that genomes across different ploidy types are highly conserved regardless the presence of local structural variations.
To investigate metabolic regulatory mechanisms, we further integrated comparative genomics and transcriptomic data by systematically comparing R. toruloides NP11 with the model yeast Saccharomyces cerevisiae S288C. Orthologous gene families were constructed to identify species-specific genes and expanded gene families. Functional enrichment analysis revealed that species-specific gene sets in R. toruloides are significantly enriched in biological processes such as the mitochondrial respiratory chain complex I pathway, xylosyltransferase-related pathways, and exopolysaccharide biosynthesis. These features may contribute to the ability of R. toruloides to maintain energetically efficient metabolic output and utilization of complex substrates.
Overall, this study provides a comprehensive dataset for future molecular engineering and systems study.
For functional annotation, we established a multi-layered annotation framework integrating homology-based prediction, InterProScan domain identification, and protein structure-based functional inference using AlphaFold3. This approach enabled comprehensive annotation and classification of protein-coding genes across the genome. Notably, proteins that are difficult to characterize using conventional methods were properly annotated. Furthermore, comparative genomic analysis of NP11 with other R. toruloides strains indicated that genomes across different ploidy types are highly conserved regardless the presence of local structural variations.
To investigate metabolic regulatory mechanisms, we further integrated comparative genomics and transcriptomic data by systematically comparing R. toruloides NP11 with the model yeast Saccharomyces cerevisiae S288C. Orthologous gene families were constructed to identify species-specific genes and expanded gene families. Functional enrichment analysis revealed that species-specific gene sets in R. toruloides are significantly enriched in biological processes such as the mitochondrial respiratory chain complex I pathway, xylosyltransferase-related pathways, and exopolysaccharide biosynthesis. These features may contribute to the ability of R. toruloides to maintain energetically efficient metabolic output and utilization of complex substrates.
Overall, this study provides a comprehensive dataset for future molecular engineering and systems study.
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