Abstract
Sandalwood oil is recognized as the queen of essential oils due to its highly valued fragrance. Globally, 16 species of sandalwood have been described among which the East Indian sandalwood, Santalum album is appreciated for superior quality and quantity of essential oils. The oils are extracted from the central dead heartwood and roots of this hemiparasitic tropical tree. Utility of sandalwood oil has been described in Ayurveda as an antiseptic and astringent. India remains the global leader in sandalwood oil production supplying 95% of the world’s requirement. Originally, harvests were made from the wild, which eventually led to over-exploitation of forests. Due to its diminishing population, S. album has been declared as a ‘vulnerable’ species. Appropriate management strategies are required for its conservation and germplasm preservation. Owing to its immense economical importance, it is imperative to generate an in depth molecular map of S. album. Integrative multi-omics data enable comprehensive understanding of biological networks and their interrelation. Comprehensive proteomic analysis provides insights into protein expression levels, allows identification of several types of post-translational modifications on proteins and aids in genome annotation. Proteogenomics workflow efficiently combines datasets derived from proteomic, genomic, and transcriptomic analyses to discover novel protein-coding genes and improve the computationally derived genome annotation. Here, we discuss the status and scope of proteogenomics in continued efforts of genome annotation of S. album.
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References
Arun Kumar AN, Srinivasa YB, Joshi G, Seetharam A (2011) Variability in and relation between tree growth, heartwood and oil content in sandalwood (Santalum album L.). Curr Sci 100:827–830
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M et al (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320:938–941
Brand JE, Norris LJ, Dumbrell IC (2012) Estimated heartwood weights and oil concentrations within 16-year-old Indian sandalwood (Santalum album) trees planted near Kununurra, Western Australia. Aust for 75:225–232
Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S et al (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25:576–583
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci USA 105:21034–21038
Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ et al (2014) An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteom 13:157–167
Celedon JM, Chiang A, Yuen MM, Diaz-Chavez ML, Madilao LL et al (2016) Heartwood-specific transcriptome and metabolite signatures of tropical sandalwood (Santalum album) reveal the final step of (Z)-santalol fragrance biosynthesis. Plant J 86:289–299
Chen MX, Zhu FY, Gao B, Ma KL, Zhang Y et al (2020) Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiol 182:1510–1526
Dasgupta MG, Ulaganathan K, Dev SA, Balakrishnan S (2019) Draft genome of Santalum album L. provides genomic resources for accelerated trait improvement. Tree Genet Genom 15:34
Datta KK, Patil AH, Patel K, Dey G, Madugundu AK et al (2016) Proteogenomics of Candida tropicalis -an opportunistic pathogen with importance for global health. OMICS 20:239–247
Diaz-Chavez ML, Moniodis J, Madilao LL, Jancsik S, Keeling CI, et al. (2013) Biosynthesis of sandalwood oil: Santalum album CYP76F cytochromes P450 produce santalols and bergamotol. PLoS One 8:e75053
Fatima T, Krishnan R, Srivastava A, Hanur VS, Rao MS (2021) Comparative transcriptome profiling of high and low oil yielding Santalum album L. bioRxiv
Grossmann J, Fernandez H, Chaubey PM, Valdes AE, Gagliardini V, et al. (2017) Proteogenomic analysis greatly expands the identification of proteins related to reproduction in the apogamous fern Dryopteris affinis ssp. affinis. Front Plant Sci 8:336
Guo X, Liu C, Zhang G, Su W, Landis JB, et al. (2020) The complete plastomes of five hemiparasitic plants (Osyris wightiana, Pyrularia edulis, Santalum album, viscum liquidambaricolum, and V. ovalifolium): comparative and evolutionary analyses within Santalales. Front Genet 11:597
Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud O (2017) Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteom 14:649–663
Jones CG, Moniodis J, Zulak KG, Scaffidi A, Plummer JA et al (2011) Sandalwood fragrance biosynthesis involves sesquiterpene synthases of both the terpene synthase (TPS)-a and TPS-b subfamilies, including santalene synthases. J Biol Chem 286:17445–17454
Kalume DE, Peri S, Reddy R, Zhong J, Okulate M et al (2005) Genome annotation of anopheles gambiae using mass spectrometry-derived data. BMC Genomics 6:128
Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS et al (2014) Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteom 13:3184–3198
Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, et al. (2011) Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteom 10:M111 011627
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis (2014) A draft map of the human proteome. Nature 509:575–581
Li Y, Zhang X, Cheng Q, Teixeira da Silva JA (2021) Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Elicitors modulate young sandalwood (Santalum album L.) growth, heartwood formation, and concrete oil synthesis. Plants (Basel) 10:339
Lu JK, Xu DP, Kang LH, He XH (2014) Host-species-dependent physiological characteristics of hemiparasite Santalum album in association with N2-fixing and nonN2-fixing hosts native to southern China. Tree Physiol 34:1006–1017
Mahesh HB, Subba P, Advani J, Shirke MD, Loganathan RM et al (2018) Multi-omics driven assembly and annotation of the sandalwood (Santalum album) genome. Plant Physiol 176:2772–2788
Marcon C, Malik WA, Walley JW, Shen Z, Paschold A et al (2015) A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes. Plant Physiol 168:233–246
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW et al (2016) A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nat Biotechnol 34:1198–1205
Mergner J, Frejno M, List M, Papacek M, Chen X et al (2020) Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579:409–414
Merrihew GE, Davis C, Ewing B, Williams G, Kall L et al (2008) Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 18:1660–1669
Meyer C, Scalzitti N, Jeannin-Girardon A, Collet P, Poch O, Thompson JD (2020) Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. BMC Bioinformatics 21
Moniodis J, Jones CG, Barbour EL, Plummer JA, Ghisalberti EL, Bohlmann J (2015) The transcriptome of sesquiterpenoid biosynthesis in heartwood xylem of Western Australian sandalwood (Santalum spicatum). Phytochemistry 113:79–86
Nesvizhskii AI (2014) Proteogenomics: concepts, applications and computational strategies. Nat Methods 11:1114–1125
Pawar H, Renuse S, Khobragade SN, Chavan S, Sathe G et al (2014) Neglected tropical diseases and omics science: proteogenomics analysis of the promastigote stage of Leishmania major parasite. OMICS 18:499–512
Pinto SM, Verma R, Advani J, Chatterjee O, Patil AH et al (2018) Integrated multi-omic analysis of Mycobacterium tuberculosis H37Ra redefines virulence attributes. Front Microbiol 9:1314
Prasad TSK, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD et al (2012) Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. J Proteome Res 11:247–260
Prasad TSK, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G et al (2017) Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 27:133–144
Renuse S, Chaerkady R, Pandey A (2011) Proteogenomics Proteomics 11:620–630
Thomson LAJ (2020) Looking ahead – global sandalwood production and markets in 2040, and implications for Pacific Island producers. Aust for 83:245–254
Walley JW, Shen Z, Sartor R, Wu KJ, Osborn J et al (2013) Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc Natl Acad Sci USA 110:E4808-4817
Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M et al (2014) Mass-spectrometry-based draft of the human proteome. Nature 509:582–587
Yang D, Qiu Q, Xu L, Xu Y, Wang Y (2020) The complete chloroplast genome sequence of Santalum album. Mitochondrial DNA B Resour 5:406–407
Zhang X, Berkowitz O, Teixeira da Silva JA, Zhang M, Ma G, Whelan J, Duan J (2015) RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album. Front Plant Sci 6:661
Zhang X, Niu M, Teixeira da Silva JA, Zhang Y, Yuan Y et al (2019) Identification and functional characterization of three new terpene synthase genes involved in chemical defense and abiotic stresses in Santalum album. BMC Plant Biol 19:115
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Subba, P., Prasad, T.S.K. (2022). Scope of Proteogenomic Analysis for Indian Sandalwood (Santalum Album). In: Gowda, M., Mahesh, H., Kole, C. (eds) The Sandalwood Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-93394-4_9
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DOI: https://doi.org/10.1007/978-3-030-93394-4_9
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