Abstract
Teak is known as one of the world’s premier hardwood tree species. However, despite the commercial interest and the large number of scientific investigations, comprehensive understanding on the genetic, molecular, and biochemical processes of this species has only recently begun to be explored. Functional genomics is the field of molecular biology that utilizes widespread combination of genetic information (e.g., enhancer DNA and non-coding RNA) and genome modification technologies to understand interactions between genes and functional regulatory elements. These technologies have emerged as a novel way to understand plant gene functions. Importance of teak has propelled various studies on transcriptomics and molecular genetics. In the last decade, transcriptomics of T. grandis of secondary wood, vegetative to flowering transition stage, and seedlings under water stress were documented. These transcriptomic studies have led to identification of genes involved in xylogenesis, production of secondary metabolites, flower formation, and drought stress. Teak transformation has not been fully achieved, but model plants are currently being used for studying several teak genes. Thus, future of functional genomics of teak is promising, particularly when the existing transcriptome data are used for wide range of analysis.
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References
Ardu S, Ameur A, Vermeesch JR, Hestand, MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168. https://doi.org/10.1093/nar/gky066
Bai X, Rivera-Vega L, Mamidala P, Bonello P, Herms D a, Mittapalli O (2011) Transcriptomic signatures of ash (Fraxinus spp.) phloem. PLoS One 6:e16368. https://doi.org/10.1371/journal.pone.0016368
Bao H, Li E, Mansfield SD, Cronk QCB, El-Kassaby Y, a, Douglas CJ, (2013) The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics 14:359. https://doi.org/10.1186/1471-2164-14-359
Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918. https://doi.org/10.1111/j.1365-313X.2007.03193.x
Brady SM, Provart NJ (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21:1034–1051. https://doi.org/10.1105/tpc.109.066050
Camel V, Galeano E, Carrer H (2017) Análisis in silico y expresión génica del factor de transcripción TgNAC01 implicado en xilogénesis y estrés abiótico en Tectona grandis. Acta Biológica Colomb 22:359–369
Carvalho A, Paiva J, Louzada J, Lima-Brito J (2013) The transcriptomics of secondary growth and wood formation in conifers. Mol Biol Int 974324. https://doi.org/10.1155/2013/974324
Chang P, Zhu L, Zhao M, Li C, Zhang Y, Li L (2019) The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development. Biotech Biotech Equip 33:967–973. https://doi.org/10.1080/13102818.2019.1632739
Chen X, Zhang J, Liu Q, Guo W, Zhao T (2014) Transcriptome sequencing and identification of cold tolerance genes in hardy corylus species (C. heterophylla Fisch) floral buds. Plos One 9:9-e108604. https://doi.org/10.1371/journal.pone.0108604
Chen BW, Xiao YF, Li JJ, Liu HL, Qin ZH, Gai Y, Jiang XN (2016) Identification of the CAD gene from Eucalyptus urophylla GLU4 and its functional analysis in transgenic tobacco. Genet Mol Res 15(4). https://doi.org/10.4238/gmr15049062
Corredoira E, Ballester A, Ibarra M, Vieitez AM (2015) Induction of somatic embryogenesis in explants of shoot cultures established from adult Eucalyptus globulus and E. saligna × E. maidenii trees. Tree Physiol 35:678–690. https://doi.org/10.1093/treephys/tpv028
Diningrat DS, Widiyanto SM, Pancoro A, Shim D, Panchangam B, Carlson JE (2015) Transcriptome of teak (Tectona grandis, L.f) in vegetative to generative stages development. J Plant Sci 10:1–14. https://doi.org/10.3923/jps.2015.1.14
Du N, Pijut PM (2010) Isolation and characterization of an AGAMOUS homolog from Fraximus pennsylvanica. Plant Mol Biol Rep 28:344–351. https://doi.org/10.1007/s11105-009-0163-7
El-Gebali S, Mistry J, Bateman A et al (2019) The Pfam protein families database in 2019. Nucleic Acids Res 47:D427–D432. https://doi.org/10.1093/nar/gky995
Fehér A (2019) Callus, dedifferentiation, totipotency, somatic embryogenesis: What these terms mean in the era of molecular plant biology Front Plant Sci 10:1–11. https://doi.org/10.3389/fpls.2019.00536
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:29–37. https://doi.org/10.1093/nar/gkr367
Galeano E, Vasconcelos TS, Carrer H (2018) Characterization of cinnamyl alcohol dehydrogenase gene family in lignifying tissues of Tectona grandis L.F. Silvae Genet 67:1–11. https://doi.org/10.2478/sg-2018-0001
Galeano E, Vasconcelos TS, De Oliveira PN, Carrer H (2019) Physiological and molecular responses to drought stress in teak (Tectona grandis L.f.). PLoS ONE 14:1–26. https://doi.org/10.1371/journal.pone.0221571
Galeano E, Vasconcelos TS, Ramiro DA, et al (2014) Identification and validation of quantitative real-time reverse transcription PCR reference genes for gene expression analysis in teak (Tectona grandis L.f.). BMC Res Notes 7:464. https://doi.org/10.1186/1756-0500-7-464
Galeano E, Vasconcelos TS, Vidal M et al (2015) Large-scale transcriptional profiling of lignified tissues in Tectona grandis. BMC Plant Biol 15:221. https://doi.org/10.1186/s12870-015-0599-x
Garcia RA, De Oliveira JL, Do Nascimento AM, De Figueiredo JVL (2014) Estabilidade de cor da madeira de teca tratada termicamente com as intempéries. Maderas Cienc Tecnologia 16(4):453–462
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. https://doi.org/10.1038/nrg.2016.49
Guan Y, Li SG, Fan XF, Su ZH (2016) Application of somatic embryogenesis in woody plants. Front Plant Sci 7:1–12. https://doi.org/10.3389/fpls.2016.00938
Haft DH, Selengut JD, Richter RA et al (2013) TIGRFAMs and genome properties in 2013. Nucleic Acids Res 41:387–395. https://doi.org/10.1093/nar/gks1234
Heredia UL, Polett LV (2016) RNA-seq analysis in forest tree species: bioinformatic problems and solutions. Tree Genet Genomes 12:30. https://doi.org/10.1007/s11295-016-0995-x
Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN (2008) Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytol 178:103–122. https://doi.org/10.1111/j.1469-8137.2007.02346.x
Hurtado FMM, Pinto M de S, de Oliveira PN, et al (2020) Analysis of NAC domain transcription factor genes of Tectona grandis L.f. involved in secondary cell wall deposition. Genes (Basel) 11. https://doi.org/10.3390/genes11010020
Jazayeri SM, Melgarejo Muñoz LM, Romero HM (2015) RNA-Seq: a glance at technologies and methodologies. Acta Biol Colomb 20(2):23–35. https://doi.org/10.15446/abc.v20n2.43639
Jones P, Binns D, Chang HY et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240. https://doi.org/10.1093/bioinformatics/btu031
Kono N, Arakawa (2019) Nanopore sequencing: review of potential applications in functional genomics. Develop Growth Differ 61:316–326. https://doi.org/10.1111/dgd.12608
Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149:461–473. https://doi.org/10.1104/pp.108.125989
Lacret R, Varela RM, Molinillo JMG, Nogueiras C, Macías F. Anthratectone and naphthotectone, two quinones from bioactive extracts of Tectona grandis (2011) J Chem Ecol 37:1341–8. https://doi.org/10.1007/s10886-011-0048-8.
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680. https://doi.org/10.1038/nbt1296-1675
Lynch M, Conery J (2000) The evolutionary fate and consequences of duplicate genes. Science 290:5494–1151–5. https://doi.org/10.1126/science.290.5494.1151
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. https://doi.org/10.1038/nature03959
Martinez M (2011) Plant protein-coding gene families: Emerging bioinformatics approaches. Trends Plant Sci 16:558–567. https://doi.org/10.1016/j.tplants.2011.06.003
Matias Hurtado FM (2020) Characterization of NAC transcription factor family of Tectona grandis involved in secondary cell wall deposition and stress response. 83p. Dissertação (Mestrado em Fisiologia e Bioquímica de Plantas), Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba
Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31–46. https://doi.org/10.1038/nrg2626
Michler CH, Bauer EO (1991) High frequency somatic embryogenesis from leaf tissue of Populus spp. Plant Sci 77:111–118. https://doi.org/10.1016/0168-9452(91)90186-C
Mustari E, Diningrat DS, Ratnasih R, Widiyanto SM (2016) APETALA2 and APETALA3 genes expression profiling on floral development of teak (Tectona grandis Linn f.). J Plant Sci 11:61–68. https://doi.org/10.3923/jps.2016.61.68
Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecology 17:3599–3613. https://doi.org/10.1111/j.1365-294X.2008.03840.x
Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Rev Genet 12:111–122. https://doi.org/10.1038/nrg2931
Norwati A, Norlia B, Rosli HM et al (2011) Development of transgenic teak (Tectona grandis) expressing a cry1AB genefor control of the skeletoniser. Asia-Pacific J Mol Biol Biotechnol 19:149–156
Oliveira PN (2021) Functional studies of Tectona grandis genes involved in the formation of wood and tolerance to environmental variation. 119p. Tese (Doutorado em Fisiologia e Bioquímica de Plantas), Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 2021
Onwimol P, Chanprame S, Chanprame S (2017) Agrobacterium-mediated transformation of cry1ab gene into Tectona grandis L. (Teak). J Int Soc Southeast Asian Agric Sci 23:68–78
Qiu Q, Ma T, Hu Q, Liu B, Wu Y, Zhou H et al. (2011) Genome-scale transcriptome analysis of the desert poplar, Populus euphratica. Tree Physiol 31:452–61 https://doi.org/10.1093/treephys/tpr015
Quiala E, Cañal MJ, Rodríguez R, Yagüe N, Chávez M, Barbón R, et al. (2012) Proteomic profiling of Tectona grandis L. leaf. Proteomics 12:1039–44. https://doi.org/10.1002/pmic.201100183
Rao G, Sui J, Zeng Y, He C, Duan A, Zhang J. (2014) De Novo Transcriptome and small rna analysis of two chinese willow cultivars reveals stress response genes in Salix matsudana. PLoS One 9:e109122. https://doi.org/10.1371/journal.pone.0109122
Ren C, Liu X, Zhang Z et al. (2016) CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Sci Rep 6:32289. https://doi.org/10.1038/srep32289
Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA et al. (2017) DNA sequencing at 40: past, present and future. Nature 550:345–353. https://doi.org/10.1038/nature24286
Sigrist CJA, De Castro E, Cerutti L et al (2013) New and continuing developments at PROSITE. Nucleic Acids Res 41:344–347. https://doi.org/10.1093/nar/gks1067
Smertenko A, Bozhkov PV (2014) Somatic embryogenesis: life and death processes during apical-basal patterning. J Exp Bot 65:1343–1360. https://doi.org/10.1093/jxb/eru005
Songstad DD, Petolino JF, Voytas DF, Reichert NA (2017) Genome editing of plants. CRC Crit Rev Plant Sci 36:1–23. https://doi.org/10.1080/07352689.2017.12816633
Sontikun Y, Chanprame S, Srinives P, Chanprame S (2013) Optimization of transient β-glucuronidase (gus) gene expression in teak (Tectona grandis L.f.) by agrobacterium tumefaciens-mediated transformation system. J Int Soc Southeast Asian Agric Sci 19:49–57
Tang Q, Ma XJ, Mo CM, Wilson IW, Song C, Zhao H et al. (2011) An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNAseq and digital gene expression analysis. BMC Genomics 12:343. https://doi.org/10.1186/1471-2164-12-343
Tang S, Dong Y, Liang D, Zhang Z et al. (2015) Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing. Plant Mol Biol Rep 33:424–438. https://doi.org/10.1007/s11105-014-0759-4
Thumma BR, Sharma N, Southerton SG (2012) Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection. BMC Genomics 13:364. https://doi.org/10.1186/1471-2164-13-364
Tripathi AM, Yadav A, Saikia SP, Roy S (2017) Global gene expression pattern in a forest tree species, Tectona grandis (Linn. F.), under limited water supply Tree Genet Genomes 13:66. https://doi.org/10.1007/s11295-017-1151-y
Tuskan GA, DiFazio SP, Teichmann T (2004) Poplar genomics is getting popular: the impact of the poplar genome project on tree research. Plant Biol 6:2–4. https://doi.org/10.1055/s-2003-44715
Van Verk MC, Hickman R, Pieterse CMJ, Van Wees SCM (2013) RNA-Seq: revelation of the messengers. Trends Plant Sci 18:175–9. https://doi.org/10.1016/j.tplants.2013.02.001
Velculescu, VE, Zhang L, Vogelstein B, Kinzler KW. (1995) Serial analysis of gene expression. Science 270:484–487. https://doi.org/10.1126/science.270.5235.484
Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17:1636–1647. https://doi.org/10.1111/j.1365-294X.2008.03666.x
Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, et al (2016) Unveiling the complexity of the maize transcriptome by singlemolecule long-read sequencing. Nat Commun 7:11708. https://doi.org/10.1038/ncomms11708
Wang X, Song J, Xing J-H et al. (2020) Genome-wide identication and expression pro le analysis of WRKY family genes in teak (Tectona grandis). Res Sq 1–27. https://doi.org/10.21203/rs.3.rs-108100/v1
Widiyanto SN, Sukmawan A, Haro N, Rahmania H (2009) Transient expression of β-glucuronidase reporter gene in Agrobacterium-inoculated shoots of various teak clones. Afr J Biotechnol 8:2143–2150. https://doi.org/10.5897/AJB09.064
Xiang LX, He D, Dong WR, Zhang YW, Shao JZ. (2010) Deep sequencing based transcriptome profiling analysis of bacteria-challenged lateolabrax japonicas reveals insight into the immune-relevant genes in marine fish. BMC Genomics 11:472. https://doi.org/10.1186/1471-2164-11-472
Yang L-T, Zhou, Y-F, Wang Y-Y et al (2019) Magnesium deficiency induced global transcriptome change in Citrus sinensis leaves revealed by RNA-Seq. Int J Mol Sci 20:3129. https://doi.org/10.3390/ijms20133129
Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR, Abel N, Binai N, Rajashekar B, Bachpai VKW, Pillai C, Dev AS (2018) Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Res 25(4):409–419. https://doi.org/10.1093/dnares/dsy013
Zhang Y, Clemens A, Maximova SN, Guiltinan MJ (2014) The Theobroma cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation. BMC Plant Biol 14:1–16. https://doi.org/10.1186/1471-2229-14-106
Zhao D, Hamilton JP, Bhat WW et al (2019) A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience 8:1–10. https://doi.org/10.1093/gigascience/giz005
Zhu J, He F, Hu S, Yu J (2008) On the nature of juman housekeeping genes. Trends Genet 24:478–481. https://doi.org/10.1016/j.tig.2008.07.006
Zortéa-Guidolin MEB, Demiate IM, Godoy RCB, Scheer AP, Grewell D, Jane J-l (2017) Structural and functional characterization of starches from Brazilian pine seeds (Araucaria angustifolia). Food Hydrocolloids 63:19–26. https://doi.org/10.1016/j.foodhyd.2016.08.022
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This research was funded by São Paulo Research Foundation (FAPESP), grant PITE/FAPESP number 2015/50634-1.
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de Oliveira, P.N., Matias, F., Galeano, E., Carrer, H. (2021). Functional Genomics of Teak. In: Ramasamy, Y., Galeano, E., Win, T.T. (eds) The Teak Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-79311-1_16
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