Haplotype Genome Assembly And Analysis Of Terpenoid Synthase Gene Family In Santalum Album

Sandalwood(Santalum album L.)is a slow-growing tropical tree with semiparasitic roots,its heartwood and sandalwood oil have high economic and medical value.The main aromatic substances in sandalwood oil are α-santalol and β-santalol,which belong to sesquiterpenoids,and terpenoid synthases(TPS)are key enzymes in its synthetic pathway.In this study,we combined various sequencing techniques to construct the chromosome-level haplotype genome of sandalwood,explored the sequence characteristics of the sandalwood genome,and focused on the bioinformatics analysis of the sandalwood TPS gene family.(1)Based on Pac Bio CCS data,Hi-C data and Illumina data obtained by whole genome sequencing,two high-quality haplotype genomes of sandalwood were constructed successfully.The haplotype-1/2 genome sizes were 223.94 Mb and 219.63 Mb,respectively,mounted on 10 chromosomes,and scaffold N50 were 26.74 Mb and25.75 Mb,respectively.Quality evaluation results showed that haplotype-1/2 genome had high integrity,98.10% and 98.00%,respectively.(2)The results of genome annotation showed that the repeat proportion of haplotype-1/2 genome was 35.69% and 34.21%,respectively,and the long terminal repeat(LTR)elements dominant,and the GC content was 38.02% and 34.83%,respectively.In addition,the results of tandem repeat(TR)analysis indicated that Cent S(TR with a monomer of 150bp)was the characteristic sequence of the centromere region of sandalwood.Meanwhile,the density distribution of LTR elements showed that Copia-type LTR enriched in the same region as Cent S on the chromosome,which helped to verify this result.(3)Based on 50 homologous genes of reported TPS genes in haplotype-1/2genome.And combined with the map of homozygous/heterozygous distribution region,it was found that most TPS genes were heterozygous genotypes.Phylogenetic analysis showed that TPS genes of sandalwood were divided into two subgroups,among which TPS-a subfamily was the largest TPS gene family.The conservative motifs analysis showed that Motif1 and Motif6 were the most conserved motifs in hap1＿TPS and hap2＿TPS,respectively.Further combined with evolutionary relationships,it was found that TPS-a family members were relatively conserved in sandalwood.Chromosome mapping analysis showed that TPS genes of sandalwood were concentrated in a few sites in the genome and showed a large number of replication phenomena,indicating that they had expanded during the process of evolution,which contributed to the formation of sandalwood aroma substances.In conclusion,this study constructed the chromosome level genome of sandalwood for the first time,providing a good genomic resource for Santalaceae species.The characteristic sequence of sandalwood centromeres was explored for the first time,which provided a clear direction for in-depth study of functional centromeres.The systematic analysis of the characteristics of the TPS gene family of sandalwood provided an important reference for the future design of in vitro synthesis of santalol,and provided useful information for the analysis of the biosynthesis mechanism of santalol.