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Transcriptomic analysis of high oil-yielding cultivated white sesame and low oil-yielding wild black sesame seeds reveal differentially expressed genes for oil and seed coat colour

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Abstract

Sesame is a well-known and primordial oilseed crop. The commonly cultivated Indian sesame (S. indicum) seed accumulates more than 50% oil and is pale yellow in colour at maturity. On the contrary, wild S. mulayanum is a low oil-containing (< 50%) genotype, with brownish black seed coat colour. The genic foundation of sesame oil quantity, quality and seed coat colour remains poorly known due to its intricacy. The present study examines the transcriptome of developing seeds from two sesame types, S. indicum and S. mulayanum, and sheds insight on the genes involved in oil biosynthesis and seed coat colour. We have carried out RNA sequencing of developing seeds at 10 and 30 DAP (days after pollination) from two genotypes and performed differential expression study. The high oil containing cultivated sesame revealed high expression of the key lipid biosynthesis genes like acetyl-CoA carboxylase, glycerol-3-phosphate acyltransferase, choline phospho transferase, GDSL esterase or lipase, lipid transfer protein, and carboxylesterase. Furthermore, many transcription factors were differentially expressed during seed maturation, including bHLH30, PIF1, ASIL2, and WRKY. The genes controlling seed coat colour included polyphenol oxidases, NAC domain-containing protein 43, and pentatricopeptide repeat-containing proteins. Several transcription factors controlling anthocyanin biosynthesis, such as GATA 18-like90, zinc finger protein, WRKY, PIF1, and ASIL2 showed significant alterations in their expression levels. This study generated a considerable transcriptome dataset and gene list controlling oil production and seed coat colour modulation in sesame, which we envisage to validate through functional studies.

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Data availability

The raw illumina sequences were deposited as FASTQ format in the NCBI Sequence Read Archive (SRA) with accession identity PRJNA644139 (accession numbers SRS6952386 and SRS6952390). The R-Script (Gene Info sorter_V4.R) used for transcriptomics data processing is available on GitHub (https://github.com/debabratadutta6/Sesame-transcriptome/blob/main/Gene%20Info%20sorter_V4.R) and is licensed under GPLv3.

References

  1. Afgan E, Baker D, Batut B, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018;46:W537–44. https://doi.org/10.1093/nar/gky379.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Altpeter F, Springer NM, Bartley LE, et al. Advancing crop transformation in the era of genome editing. Plant Cell. 2016;7:1510–20. https://doi.org/10.1105/tpc.16.00196.

    Article  CAS  Google Scholar 

  3. Andargie M, Vinas M, Rathgeb A, et al. Lignans of sesame (Sesamum indicum L.): a comprehensive review. Molecules. 2021;26:883. https://doi.org/10.3390/molecules26040883.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bhunia RK, Kaur R, Maiti MK. Metabolic engineering of fatty acid biosynthetic pathway in sesame (Sesamum indicum L.): assembling tools to develop nutritionally desirable sesame seed oil. Phytochem Rev. 2016;15:799–811. https://doi.org/10.1007/s11101-015-9424-2.

    Article  CAS  Google Scholar 

  5. Cheng FC, Jinn TR, Hou RC, et al. Neuroprotective effects of sesamin and sesamolin on gerbil brain in cerebral ischemia. Int J Biomed Sci. 2006;2:284–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Cui C, Liu Y, Liu Y, et al. Genome-wide association study of seed coat color in sesame (Sesamum indicum L.). PLoS ONE. 2021;16:e0251526. https://doi.org/10.1371/journal.pone.0251526.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. https://doi.org/10.1093/bioinformatics/bts635.

    Article  CAS  PubMed  Google Scholar 

  8. Dossa K, Diouf D, Wang L, et al. The emerging oilseed crop Sesamum indicum enters the “Omics” era. Front Plant Sci. 2017;8:1154. https://doi.org/10.3389/fpls.2017.01154.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Dossou SSK, et al. Transcriptome analysis of black and white sesame seed reveals candidate genes associated with black seed development in sesame (Sesamum Indicum). 2020, PREPRINT (Version 1) available at Research Square. https://doi.org/10.21203/rs.3.rs-46165/v1.

  10. Du H, Zhang H, Wei L, et al. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC Plant Biol. 2019;27:588. https://doi.org/10.1186/s12870-019-2172-5.

    Article  CAS  Google Scholar 

  11. Dutta D, Prasad R, Gangopadhyay G. Inter-specific hybrid sesame with high lignan content in oil reveals increased expression of sesamin synthase gene. Nucleus. 2021. https://doi.org/10.1007/s13237-021-00354-3.

    Article  Google Scholar 

  12. El-Bramawy MAES, El-Hendawy SES, Amin SWI. Assessing the suitability of morphological and phenological traits to screen Sesame genotypes for Fusarium wilt and charcoal rot disease resistance. J Plant Protect Res. 2008;48:397–410. https://doi.org/10.2478/v10045-008-0049-y.

    Article  Google Scholar 

  13. Falusi OA. Segregation of genes controlling seed colour in sesame (Sesamum indicum linn.) from Nigeria. Afr J Biotech. 2007;6:2780–3. https://doi.org/10.5897/AJB2007.000-2444.

    Article  CAS  Google Scholar 

  14. Goswami G, Nath UK, Park JI, et al. Transcriptional regulation of anthocyanin biosynthesis in a high anthocyanin resynthesized Brassica napus cultivar. J of Biol Res-Thessaloniki. 2018;25:19. https://doi.org/10.1186/s40709-018-0090-6.

    Article  CAS  Google Scholar 

  15. Hichri I, Barrieu F, Bogs J, et al. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J Exp Bot. 2011;62:2465–83. https://doi.org/10.1093/jxb/erq442.

    Article  CAS  PubMed  Google Scholar 

  16. Jeong J, Cohu C, Kerkeb L, et al. Chloroplast Fe(III) chelate reductase activity is essential for seedling viability under iron limiting conditions. Proc Natl Acad Sci. 2008;105:10619–24. https://doi.org/10.1073/pnas.0708367105.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Johnson CS, Kolevski B, Smyth DR. TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell. 2002;14:1359–75. https://doi.org/10.1105/tpc.001404.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kanu PJ. Biochemical analysis of black and white sesame seeds from China. Am J Biochem Mol Biol. 2011;1:145–57. https://doi.org/10.3923/ajbmb.2011.145.157.

    Article  Google Scholar 

  19. Ke T, Dong C, Mao H, et al. Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum). BMC Plant Biol. 2011;11:180. https://doi.org/10.1186/1471-2229-11-180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ke T, Yu J, Dong C, et al. ocsESTdb: A database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biol. 2015;15:19. https://doi.org/10.1186/s12870-014-0399-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Koes R, Verweij W, Quattrocchio F. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 2005;10:236–42. https://doi.org/10.1016/j.tplants.2005.03.002.

    Article  CAS  PubMed  Google Scholar 

  22. Lang D, Weiche B, Timmerhaus G, et al. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2010;2:488–503. https://doi.org/10.1093/gbe/evq032.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li-Beisson Y, Shorrosh B, Beisson F, et al. Acyl-lipid metabolism. Arabidopsis Book. 2013;11:e0161. https://doi.org/10.1199/tab.0161.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Li D, Liu P, Yu J, et al. Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses. BMC Plant Biol. 2017;17:152. https://doi.org/10.1186/s12870-017-1099-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30. https://doi.org/10.1093/bioinformatics/btt656.

    Article  CAS  PubMed  Google Scholar 

  26. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001;4:402–8. https://doi.org/10.1006/meth.2001.1262.

    Article  CAS  Google Scholar 

  27. Liyana-Pathirana CM, Shahidi F. Importance of insoluble-bound phenolics to antioxidant properties of wheat. J Agric Food Chem. 2006;54:1256–64. https://doi.org/10.1021/jf052556h.

    Article  CAS  PubMed  Google Scholar 

  28. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. https://doi.org/10.1186/s13059-014-0550-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Mackon E, Ma Y, Jeazet GC, et al.  Computational and transcriptomic analysis unraveled OsMATE34 as a putative anthocyanin transporter in black Rice (Oryza sativa L.) Caryopsis. Genes (Basel) 2021;12:583. https://doi.org/10.3390/genes12040583

  30. Mei H, Wei A, Liu Y, et al. Variation and correlation analysis of sesamin, oil and protein contents in sesame germplasm resources. China Oils & Fats. 2013;38:87–90.

    CAS  Google Scholar 

  31. Monforte A, Oliver M, Gonzalo M, et al. Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.). Theor Appl Genet. 2004;108:750–8. https://doi.org/10.1007/s00122-003-1483-x.

    Article  CAS  PubMed  Google Scholar 

  32. Namayandeh SM, Kaseb, Lesan S. Olive and sesame oil effect on lipid profile in hypercholesterolemic patients, which better? Int J Prev Med. 2013;4:1059–62.

    PubMed  PubMed Central  Google Scholar 

  33. Okuley J, Lightner J, Feldmann K, et al. Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell. 1994;6:147–58. https://doi.org/10.1105/tpc.6.1.147.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Pathak N, Bhaduri A, Rai AK. Sesame: bioactive compounds and health benefits. Bioact Mol Food. 2019;181–200. https://doi.org/10.1007/978-3-319-78030-6_59.

  35. Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5. https://doi.org/10.1038/nbt.3122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Pourcel L, Routaboul JM, Kerhoas L, et al. TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. Plant Cell. 2005;17:2966–80. https://doi.org/10.1105/tpc.105.035154.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Prasad R, Gangopadhyay G. Phenomic analyses of Indian and exotic accession of sesame (Sesamum indicum L.). J Plant Breed Crop Sci. 2011;3:336–52.

    Google Scholar 

  38. R Core Team. (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

  39. Shahidi F, Liyana-Pathirana CM, Wall DS. Antioxidant activity of white and black sesame seeds and their hull fractions. Food Chem. 2006;99:478–83. https://doi.org/10.1016/j.foodchem.2005.08.009.

    Article  CAS  Google Scholar 

  40. Sheng C, Song S, Zhou R, et al. QTL-Seq and transcriptome analysis disclose major QTL and candidate genes controlling leaf size in Sesame (Sesamum indicum L.). Front Plant Sci. 2021;12:580846. https://doi.org/10.3389/fpls.2021.580846.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Song Q, Joshi M, Wang S, et al. Comparative analysis of root transcriptome profiles of sesame (Sesamum indicum L.) in response to osmotic stress. J Plant Growth Regul. 2020;40:1787–801. https://doi.org/10.1007/s00344-020-10230-0.

    Article  CAS  Google Scholar 

  42. Su R, Zhou R, Mmadi MA, et al. Root diversity in sesame (Sesamum indicum L.): insights into the morphological, anatomical and gene expression profiles. Planta. 2019;250:1461–74. https://doi.org/10.1007/s00425-019-03242-y.

    Article  CAS  PubMed  Google Scholar 

  43. Szklarczyk D, Annika LG, David L, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–13. https://doi.org/10.1093/nar/gky1131.

    Article  CAS  PubMed  Google Scholar 

  44. Wang L, Dossou SSK, Wei X, et al. Transcriptome dynamics during black and white sesame (Sesamum indicum L.) seed development and identification of candidate genes associated with black pigmentation. Genes. 2020;11:1399. https://doi.org/10.3390/genes11121399.

    Article  CAS  PubMed Central  Google Scholar 

  45. Wang L, et al. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics. 2016;17:31. https://doi.org/10.1186/s12864-015-2316-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wang L, Xia Q, Zhang Y, et al. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics. 2016;17:31. https://doi.org/10.1186/s12864-015-2316-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Wang L, Yu S, Tong C, et al. Genome sequencing of the high oil crop sesame. Genome Biol. 2014;15:R39. https://doi.org/10.1186/gb-2014-15-2-r39.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Wang L, Zhang Y, Li D, et al. Gene expression profiles that shape high and low oil content sesames. BMC Genet. 2019;20:45. https://doi.org/10.1186/s12863-019-0747-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Wei W, Qi X, Wang L, et al. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics. 2011;12:451. https://doi.org/10.1186/1471-2164-12-451.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Wei X, Liu K, Zhang Y, et al. Genetic discovery for oil production and quality in sesame. Nat Commun. 2015;6:1–10. https://doi.org/10.1038/ncomms9609.

    Article  CAS  Google Scholar 

  51. Wei X, Zhu X, Yu J, et al. Identification of sesame genomic variations from genome comparison of landrace and variety. Front Plant Sci. 2016;7:1169. https://doi.org/10.3389/fpls.2016.01169.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Wu WL, Hsiao YY, Lu HC, et al. Expression regulation of MALATE SYNTHASE involved in glyoxylate cycle during protocorm development in Phalaenopsis aphrodite (Orchidaceae). Sci Rep. 2020;10:10123. https://doi.org/10.1038/s41598-020-66932-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Yu CY. Molecular mechanism of manipulating seed coat coloration in oilseed Brassica species. J Appl Genet. 2013;54:135–45. https://doi.org/10.1007/s13353-012-0132-y.

    Article  PubMed  Google Scholar 

  54. Zhang H, Miao H, Ju M. Potential for adaptation to climate change through genomic breeding in Sesame. In: Kole C, editor. Genomic designing of climate-smart oilseed crops. Cham: Springer; 2019. https://doi.org/10.1007/978-3-319-93536-2_7.

    Chapter  Google Scholar 

  55. Zhang H, Miao H, Wei L, et al. Genetic analysis and QTL mapping of seed coat color in sesame (Sesamum indicum L.). PLoS ONE. 2013;8:e63898. https://doi.org/10.1371/journal.pone.0063898.

    Article  PubMed  PubMed Central  Google Scholar 

  56. Zhang Y, Li D, Zhou R, et al. A collection of transcriptomic and proteomic datasets from sesame in response to salt stress. Data Brief. 2020;32:106096. https://doi.org/10.1016/j.dib.2020.106096.

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

DD acknowledges Dr Amit P Parikh, Department of Biotechnology (DBT), India and Purvaja Ramachandran, National Biodiversity Authority, India for providing necessary permission for carrying sesame samples to the University of York, UK. GG is indebted to the Director, Bose Institute for providing the infrastructural support and an intramural research grant. DD and GG are thankful to Mr Jadab Ghosh, Mrs Kaberi Ghosh and Mrs Sheolee Chakraborty for their technical assistance.

Funding

This work was funded by a grant (Grant Number: BT/IN/NBPP/DD/04/2018-19) under theNewton Bhabha PhD Placement Programme, jointly supported by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India and the British Council, UK.

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Authors and Affiliations

  1. Division of Plant Biology, Bose Institute (Unified Academic Campus), EN 80, Sector V, Bidhan Nagar, 700091, Kolkata, India

    Debabrata Dutta & Gaurab Gangopadhyay

  2. Department of Biology, Wentworth Way, University of York, Heslington, YO10 5DD, York, UK

    Andrea Harper

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  1. Debabrata Dutta
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Contributions

DD: Conceptualization, Methodology, Formal analysis, Investigation, Data Curation, Visualization, Writing—original draft, Funding acquisition. AH: Supervision, Resources, Project administration, Formal analysis, Data Curation, Funding acquisition. GG: Supervision, Conceptualization, Resources, Writing—original draft, Writing—review & editing, Funding acquisition.

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Correspondence to Gaurab Gangopadhyay.

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Dutta, D., Harper, A. & Gangopadhyay, G. Transcriptomic analysis of high oil-yielding cultivated white sesame and low oil-yielding wild black sesame seeds reveal differentially expressed genes for oil and seed coat colour. Nucleus 65, 151–164 (2022). https://doi.org/10.1007/s13237-022-00389-0

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