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De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L.

Published online by Cambridge University Press:  02 December 2021

Tanuja ,
Nibir Ranjan Parasar ,
Ravichandiran Kumar ,
Purushothaman Natarajan  and
Madasamy Parani Open the ORCID record for Madasamy Parani [Opens in a new window]
Tanuja
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Nibir Ranjan Parasar
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Ravichandiran Kumar
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Purushothaman Natarajan
Affiliation:
Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, USA
Madasamy Parani*
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
*
Author for correspondence: Madasamy Parani, E-mail: paranim@srmist.edu.in
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Abstract

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Keywords

Basilde novo assemblyOcimum gratissimumRNA sequencingtranscriptome
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 6 , December 2021 , pp. 469 - 476
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

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References

Airaodion, AI, Ibrahim, AH, Ogbuagu, U, Ogbuagu, EO, Awosanya, OO, Akinmolayan, JD, Njoku, OC, Obajimi, OO, Adeniji, AR and Adekale, OA (2019) Evaluation of phytochemical content and antioxidant potential of Ocimum gratissimum and Telfairia occidentalis leaves. Asian Journal of Research in Medical and Pharmaceutical Sciences 7, 1–11.Google Scholar
Andrews, S (2010) FASTQC. A quality control tool for high throughput sequence data’.Google Scholar
Barboza, JN, da Silva Maia Bezerra Filho, C, Silva, RO, Medeiros JV and de Sousa DP (2018) An overview on the anti-inflammatory potential and antioxidant profile of eugenol. Oxidative Medicine and Cellular Longevity 2018, 3957262.CrossRefGoogle ScholarPubMed
Beier, S, Thiel, T, Münch, T, Scholz, U and Mascher, M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics (Oxford, England) 33, 2583–2585.CrossRefGoogle ScholarPubMed
Casanova, LM, Gu, W, Costa, SS and Jeppesen, PB (2017) Phenolic substances from Ocimum species enhance glucose-stimulated insulin secretion and modulate the expression of key insulin regulatory genes in mice pancreatic islets. Journal of Natural Products 80, 3267–3275.CrossRefGoogle ScholarPubMed
Chaiyarat, R, Suebsima, R, Putwattana, N, Kruatrachue, M and Pokethitiyook, P (2011) Effects of soil amendments on growth and metal uptake by Ocimum gratissimum grown in Cd / Zn-contaminated soil. Water, Air, & Soil Pollution 214.1 , 383–392.CrossRefGoogle Scholar
Chand, S, Singh, S, Singh, VK and Patra, DD (2015) Utilization of heavy metal-rich tannery sludge for sweet basil (Ocimum basilicum L.) cultivation. Environmental Science and Pollution Research 22.10, 7470–7475.CrossRefGoogle Scholar
Chase, MW, Christenhusz, MJM, Fay, MF, Byng, JW, Judd, WS, Soltis, DE, Mabberley, DJ, Sennikov, AN, Soltis, PS, Stevens, PF, Briggs, Barbara, Brockington, Samuel, Chautems, Alain, Clark John, C, Conran, John, Haston, Elspeth, Möller, Michael, Moore, Michael, Olmstead, Richard, Perret, Mathieu, Skog, Laurence, Smith, James, Tank, David, Vorontsova, Maria and Weber, Anton (2016) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: aPG IV. Botanical Journal of the Linnean Society 181, 1–20.Google Scholar
Chattopadhyay, RR (1994) Anxiolytic activity of Ocimum sanctum leaf extract. Ancient Science of Life 14, 108–111.Google ScholarPubMed
Chimnoi, N, Reuk-ngam, N, Chuysinuan, P, Khlaychan, P, Khunnawutmanotham, N, Chokchaichamnankit, D, Thamniyom, W, Klayraung, S, Mahidol, C and Techasakul, S (2018) Characterization of essential oil from Ocimum gratissimum leaves: antibacterial and mode of action against selected gastroenteritis pathogens. Microbial Pathogenesis 118, 290–300.CrossRefGoogle ScholarPubMed
Dinu, C, Vasile, GG, Buleandra, M, Popa, DE, Gheorghe, S and Ungureanu, EM (2020) Translocation and accumulation of heavy metals in Ocimum basilicum L. Plants grown in a mining-contaminated soil. Journal of Soils and Sediments 20.4, 2141–2154.CrossRefGoogle Scholar
Du, YT, Zhao, MJ, Wang, CT, Gao, Y, Wang, YX, Liu, YW, Chen, M, Chen, J, Zhou, YB, Xu, ZS and Ma, YZ (2018) Identification and characterization of GmMYB118 responses to drought and salt stress. BMC Plant Biology 18, 1–18.CrossRefGoogle ScholarPubMed
Fujisawa, S and Murakami, Y (2016) Eugenol and its role in chronic diseases. Advances in Experimental Medicine and Biology 929, 45–66.CrossRefGoogle ScholarPubMed
Fu, L, Niu, B, Zhu, Z, Wu, S and Li, W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics (Oxford, England) 28, 3150–3152.CrossRefGoogle ScholarPubMed
Grabherr, MG, Haas, BJ, Yassour, M, Levin, JZ, Thompson, DA, Amit, I, Adiconis, X, Fan, L, Raychowdhury, R, Zeng, Q, Chen, Z, Mauceli, E, Hacohen, N, Gnirke, A, Rhind, N, di Palma, F, Bruce, W, Friedman, N and R, A (2013) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology 29, 644–652.CrossRefGoogle Scholar
Hamer, DH (1986) Metallothionein. Annual Review of Biochemistry 55, 913–951.CrossRefGoogle ScholarPubMed
Ighodaro, OM, Agunbiade, SO and Akintobi, O (2010) Phytotoxic and anti-microbial activities of flavonoids in Ocimum gratissimum. Life Science Journal 7, 45–48.Google Scholar
Kumar, S, Stecher, G, Li, M, Knyaz, C and Tamura, K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology Evolution 35, 1547–1549.CrossRefGoogle ScholarPubMed
Lahon, K and Das, S (2011) Hepatoprotective activity of Ocimum sanctum alcoholic leaf extract against paracetamol-induced liver damage in albino rats. Pharmacognosy Research 3, 13–18.CrossRefGoogle ScholarPubMed
Li, B and Dewey, CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.CrossRefGoogle ScholarPubMed
Lippold, F, Sanchez, DH, Musialak, M, Schlereth, A, Scheible, WR, Hincha, DK and Udvardi, MK (2009) AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis. Plant Physiology 149.4, 1761–1762.CrossRefGoogle Scholar
Luo, R, Liu, B, Xie, Y, Li, Z, Huang, W, Yuan, J, He, G, Chen, Y, Pan, Q, Liu, Y and Tang, J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 2047–217X.CrossRefGoogle ScholarPubMed
Ma, D and Constabel, CP (2019) MYB repressors as regulators of phenylpropanoid metabolism in plants. Trends in Plant Science 24, 275–289.CrossRefGoogle ScholarPubMed
Manaharan, T, Thirugnanasampandan, R, Jayakumar, R, Ramya, G, Ramnath, G and Kanthimathi, MS (2014) Antimetastatic and anti-inflammatory potentials of essential oil from edible Ocimum sanctum leaves. Scientific World Journal 239508, 5 pages.Google Scholar
Martin, M (2011) CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal 17.1, 10–12.CrossRefGoogle Scholar
Olamilosoye, KP, Akomolafe, RO, Akinsomisoye, OS, Adefisayo, MA and Alabi, QK (2018) The aqueous extract of Ocimum gratissimum leaves ameliorates acetic acid-induced colitis via improving antioxidant status and hematological parameters in male Wistar rats. Egyptian Journal of Basic and Applied Sciences 5, 220–227.CrossRefGoogle Scholar
Parasuraman, S, Balamurugan, S, Christapher, PV, Petchi, RR, Yeng, WY, Sujithra, J and Vijaya, C (2015) Evaluation of antidiabetic and antihyperlipidemic effects of hydroalcoholic extract of leaves of Ocimum tenuiflorum (Lamiaceae) and prediction of biological activity of its phytoconstituents. Pharmacognosy Research 7, 156–165.CrossRefGoogle ScholarPubMed
Pattanayak, P, Behera, P, Das, D and Panda, S (2010) Ocimum sanctum Linn. A reservoir plant for therapeutic applications: an overview. Pharmacognosy Reviews 4, 95–105.CrossRefGoogle Scholar
Pyne, RM, Honig, JA, Vaiciunas, J, Wyenandt, CA and Simon, JE (2018) Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm. BMC Plant Biology 18, 1–15.CrossRefGoogle ScholarPubMed
Rastogi, S, Meena, S, Bhattacharya, A, Ghosh, S, Shukla, RK, Sangwan, NS, Lal, RK, Gupta, MM, Lavania, UC, Gupta, V and Nagegowda, DA (2014) De novo sequencing and comparative analysis of holy and sweet basil transcriptomes. BMC Genomics 15, 1–18.CrossRefGoogle ScholarPubMed
Rastogi, S, Kalra, A, Gupta, V, Khan, F, Lal, RK, Tripathi, AK, Parameswaran, S, Gopalakrishnan, C, Ramaswamy, G and Shasany, AK (2015) Unravelling the genome of holy basil: an “incomparable” “elixir of life” of traditional Indian medicine. BMC Genomics 16, 413.CrossRefGoogle ScholarPubMed
Saharkhiz, MJ, Kamyab, AA, Kazerani, NK, Zomorodian K, Pakshir K and Rahimi MJ (2014) Chemical compositions and antimicrobial activities of Ocimum sanctum L. Essential oils at different harvest stages. Jundishapur Journal of Microbiology 8, 1–7.CrossRefGoogle ScholarPubMed
Singh, P, Jayaramaiah, RH, Agawane, SB, Vannuruswamy, G, Korwar, AM, Anand, A, Dhaygude, VS, Shaikh, ML, Joshi, , Boppana, R and Kulkarni, MJ (2016) Potential dual role of eugenol in inhibiting advanced glycation end products in diabetes: proteomic and mechanistic insights. Scientific Reports 6, 1–13.Google ScholarPubMed
Srivastava, S, Adholeya, A, Conlan, XA and Cahill, DM (2016) Acidic potassium permanganate chemiluminescence for the determination of antioxidant potential in three cultivars of Ocimum basilicum. Plant Foods for Human Nutrition 71, 72–80.CrossRefGoogle ScholarPubMed
Sumitha K, V and Thoppil, JE (2016) Larvicidal efficacy and chemical constituents of O. gratissimum L. (Lamiaceae) essential oil against aedes albopictus skuse (Diptera: Culicidae). Parasitology Research 115, 673–680.CrossRefGoogle Scholar
Thompson, JD, Gibson, TJ and Higgins, DG (2003) Multiple sequence alignment using ClustalW and ClustalX. Current protocols in bioinformatics. Chapter 2: Unit 2.3.Google Scholar
Torre, S, Tattini, M, Brunetti, C, Guidi, L, Gori, A, Marzano, C, Landi, M and Sebastiani, F (2016) De novo assembly and comparative transcriptome analyses of red and green morphs of sweet basil grown in full sunlight. PLoS ONE 11, 1–19.CrossRefGoogle ScholarPubMed
Upadhyay, AK, Chacko, AR, Gandhimathi, A, Ghosh, P, Harini, K, Joseph, AP, Joshi, AG, Karpe, SD, Kaushik, S, Kuravadi, N and Lingu, CS (2015) Genome sequencing of herb tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biology 15, 1–20.CrossRefGoogle ScholarPubMed
Van Bel, M, Diels, T, Vancaester, E, Kreft, L, Botzki, A, Van de Peer, Y, Coppens, F and Vandepoele, K (2018) PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Research 46.D1, 1190–1196.CrossRefGoogle Scholar
Vogt, T (2010) Phenylpropanoid biosynthesis. Molecular Plant 3, 2–20.CrossRefGoogle ScholarPubMed
Zerbino, DR and Birney, E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18, 821–829.CrossRefGoogle Scholar
Zhan, X, Yang, L, Wang, D, Zhu, JK and Lang, Z (2016) De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress. BMC Genomics 17, 1–12.CrossRefGoogle ScholarPubMed
Zhao, QY, Wang, Y, Kong, YM, Luo, D, Li, X and Hao, P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12, 1–12.CrossRefGoogle ScholarPubMed
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