Abstract
Camptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Here, we report a high-quality, chromosome-level C. acuminata genome assembly. We find that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. Comparing with Catharanthus roseus, the loganic acid O-methyltransferase (LAMT) in C. acuminata fails to convert loganic acid into loganin. Instead, two secologanic acid synthases (SLASs) convert loganic acid to secologanic acid. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contribute greatly to the camptothecin biosynthesis in C. acuminata. Our results emphasize the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.
Highlights
Camptothecin and its derivatives are widely used for treating malignant tumors
We aim to address how camptothecin biosynthesis has evolved by conversion of the same intermediate chemical into different subsequent products comparing with vinblastine/vincristine biosynthesis in C. roseus[14,25]
The previously published C. acuminata genome assembly (Cac genome assembly v2.4) was created with the ALLPATHS-LG assembler using Illumina short-read technology, producing an assembly of 1,394 scaffolds (5,219 contigs) spanning 403.2 Mb, with a scaffold N50 of 1.75 Mb26. To improve this short-reads-based assembly, we re-sequenced and assembled the genome of C. acuminata using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio), improving the accuracy of the assembly obtained from the Illumina platform
Summary
Camptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Both pathways synthesize complex intermediate organic molecules (e.g., geraniol, 8-oxogeranial[12,13,14], iridodial15, 7-deoxyloganetic acid16, 7-deoxyloganic acid, and loganic acid17) using the same set of enzymes, which are presumably encoded by homologous genes After these intermediate stages, the two biosynthetic pathways are quite different from each other. We identify an independent whole-genome duplication (WGD) event in this high-quality chromosomal-scale genome We use this reference genome to identify genes associate with the evolutionary origin of camptothecin biogenesis by means of comprehensive homology searching, gene family analyses, co-expression analyses of RNA-seq datasets and functional verification of site mutations in key homologous genes.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
