Presentation Information
[P04-559]Comparative genome analysis of the green alga Tetraselmis sp. NKG400013 reveals the genetic basis of glycosphingolipid biosynthesis
○Rein Yasui1, Atsushi Arakaki1, Kosuke Kataoka1,2, Tsuyoshi Tanaka1 (1. Graduate School of Engineering, Tokyo University of Agriculture and Technology (Japan), 2. Comprehensive Research Organization, Waseda University (Japan))
Keywords:
Glycosphingolipid,Marine microalgae,Comparative genomics
[Purpose]
Microalgae are promising hosts for the sustainable production of valuable compounds. Glycosphingolipids are useful substances used as ingredients in cosmetics and dietary supplements. While glycosphingolipid production has been reported in microalgae, understanding of the relevant genes is limited, and the genetic basis of glycosphingolipid biosynthesis has not been completely clarified. This study aims to characterize the genome architecture of the green alga Tetraselmis sp. NKG400013 and to gain insights into glycosphingolipid biosynthetic pathways via genome sequencing and comparative genomic analysis.
[Method]
Genome assembly was performed using hifiasm with PacBio HiFi sequencing data, followed by the removal of haplotigs. Genes were predicted with BRAKER3 using RNA-seq data, and functional annotation was conducted with InterProScan and eggNOG-mapper. Repetitive elements were identified using RepeatModeler and RepeatMasker. Candidate genes involved in glycosphingolipid biosynthesis were identified by BLASTp (E-value is less than or equal to 1×10-25) and reciprocal best-hit analyses using Arabidopsis thaliana proteins as queries. Comparative analyses across green algae were conducted using OrthoFinder.
[Results & Consideration]
The assembled genome was approximately 423.8 Mb, with 81.2% complete BUSCOs. The genome contains 76.3% repetitive sequences, predominantly consisting of LTR retrotransposons. Comparative analysis across green algae revealed a significant positive association between genome size and repeat content, indicating that repeat expansion has contributed to genome expansion in Tetraselmis. Phylogenetic analysis based on single-copy orthologs placed NKG400013 within the Chlorodendrophyceae clade, and the overall phylogenetic relationships among the examined green algae were consistent with previous reports. Seven enzymes involved in glycosphingolipid biosynthesis were identified based on sequence homology. These enzymes were predicted to localize to the endoplasmic reticulum, consistent with their localization in other eukaryotes. Comparative analysis of these seven enzymes across 11 green algal species showed that enzymes related to ceramide synthesis were conserved across most species. In contrast, sphingolipid Δ4 and Δ8 desaturases exhibited variable patterns: Tetraselmis species possessed both enzymes, whereas most other green algal lineages retained only one or lacked both.
[Conclusion]
This study provides insights into glycosphingolipid biosynthesis in Tetraselmis. Comparative genomic analysis revealed that genes involved in ceramide synthesis are conserved in most green algae, while sphingolipid Δ4 and Δ8 desaturases exhibit diverse distribution patterns. These findings provide a basis for future studies on sphingolipid metabolism.
Microalgae are promising hosts for the sustainable production of valuable compounds. Glycosphingolipids are useful substances used as ingredients in cosmetics and dietary supplements. While glycosphingolipid production has been reported in microalgae, understanding of the relevant genes is limited, and the genetic basis of glycosphingolipid biosynthesis has not been completely clarified. This study aims to characterize the genome architecture of the green alga Tetraselmis sp. NKG400013 and to gain insights into glycosphingolipid biosynthetic pathways via genome sequencing and comparative genomic analysis.
[Method]
Genome assembly was performed using hifiasm with PacBio HiFi sequencing data, followed by the removal of haplotigs. Genes were predicted with BRAKER3 using RNA-seq data, and functional annotation was conducted with InterProScan and eggNOG-mapper. Repetitive elements were identified using RepeatModeler and RepeatMasker. Candidate genes involved in glycosphingolipid biosynthesis were identified by BLASTp (E-value is less than or equal to 1×10-25) and reciprocal best-hit analyses using Arabidopsis thaliana proteins as queries. Comparative analyses across green algae were conducted using OrthoFinder.
[Results & Consideration]
The assembled genome was approximately 423.8 Mb, with 81.2% complete BUSCOs. The genome contains 76.3% repetitive sequences, predominantly consisting of LTR retrotransposons. Comparative analysis across green algae revealed a significant positive association between genome size and repeat content, indicating that repeat expansion has contributed to genome expansion in Tetraselmis. Phylogenetic analysis based on single-copy orthologs placed NKG400013 within the Chlorodendrophyceae clade, and the overall phylogenetic relationships among the examined green algae were consistent with previous reports. Seven enzymes involved in glycosphingolipid biosynthesis were identified based on sequence homology. These enzymes were predicted to localize to the endoplasmic reticulum, consistent with their localization in other eukaryotes. Comparative analysis of these seven enzymes across 11 green algal species showed that enzymes related to ceramide synthesis were conserved across most species. In contrast, sphingolipid Δ4 and Δ8 desaturases exhibited variable patterns: Tetraselmis species possessed both enzymes, whereas most other green algal lineages retained only one or lacked both.
[Conclusion]
This study provides insights into glycosphingolipid biosynthesis in Tetraselmis. Comparative genomic analysis revealed that genes involved in ceramide synthesis are conserved in most green algae, while sphingolipid Δ4 and Δ8 desaturases exhibit diverse distribution patterns. These findings provide a basis for future studies on sphingolipid metabolism.
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