Draft genome of Santalum album L. provides genomic resources for accelerated trait improvement

  • Modhumita Ghosh DasguptaEmail author
  • Kandasamy Ulaganathan
  • Suma Arun Dev
  • Swathi Balakrishnan
Original Article
Part of the following topical collections:
  1. Genome Biology


Sandalwood (Santalum album L.) is a valuable commodity in the international trade due to its use in fragrance and essential oil industries. In the present study, a draft genome of S. album representing the natural population from Kerala, India, was sequenced and assembled into 74,900 major scaffolds with N50 of 12,068 bp and the estimated genome size was 286 Mb. A total of 37,500 genes were predicted including 30 genes from terpene synthase gene family. Repetitive sequence was mined and spanned 12.52% of the sandalwood genome. Domain analysis of predicted proteins revealed that transcription factors and kinases were the major category of proteins followed by ARM repeat proteins and WD domain proteins. The draft genome encoded for 574 miRNAs belonging to 23 families including two miRNAs associated with terpenoid biosynthesis pathway. Further, the consensus chloroplast genome of 147.25 kb size was reconstructed and phylogenetic analysis with 40 plastid genes grouped members of Santalales with Asterids in accordance with its taxonomic status recommended in APG III and APG IV. Variant calling was conducted against the published genome and a total of 1,191,838 (0.42%) SNPs and 98,312 (0.034%) InDels were predicted in the present genome. The draft genome presented in this study has provided additional genomic resource for S. album for subsequent research in population diversity estimation and accelerated trait breeding in this species.


Chloroplast genome Genome sequencing microRNA Sandalwood Terpene synthase 



The authors acknowledge the Indian Council of Forestry Research and Education, Dehra Dun, India for funding the research work.

Data archiving statement

The raw sequence reads of whole genome is deposited in the NCBI SRA database with accession number SRP145575.

Author contributions

MGD conceived, planned, designed the experiments, and finalized the manuscript; KU conducted the genome assembly and annotation; SAD and SB conducted the SSR genotyping and phylogenetic analysis. All authors have contributed towards manuscript writing and read and approved the final manuscript.


This study was funded by Indian Council of Forestry Research and Education, Dehra Dun, India.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11295_2019_1334_MOESM1_ESM.docx (30 kb)
Supplementary Tables 1, 2, 3, 5 (DOCX 30 kb)
11295_2019_1334_MOESM2_ESM.xlsx (116 kb)
Supplementary Table 4 (XLSX 116 kb)
11295_2019_1334_MOESM3_ESM.xlsx (10.2 mb)
Supplementary Table 6 (XLSX 10422 kb)
11295_2019_1334_MOESM4_ESM.vcf (232.4 mb)
Supplementary File 1 Variants (SNPs and InDels) predicted across the two draft genomes of S. album (VCF 238010 kb)
11295_2019_1334_MOESM5_ESM.docx (523 kb)
Supplementary Figures 1, 2, 3 (DOCX 523 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Division of Plant Biotechnology and CytogeneticsInstitute of Forest Genetics and Tree BreedingCoimbatoreIndia
  2. 2.Centre for Plant Molecular BiologyOsmania UniversityHyderabadIndia
  3. 3.Forest Genetics and Biotechnology DivisionKerala Forest Research InstituteThrissurIndia

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