Skip to main content
SpringerLink
Log in

Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts in Ailanthus excelsa Roxb., a multi-purpose tropical tree species

  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

Safety matches are an essential consumer commodity which faces considerable shortage of raw material due to specific requirements like color, wax stability, consistent burning and splinting ability in wood. Ailanthus excelsa Roxb. is a multi-purpose tropical tree species which is predominantly used for production of match splints. It is a data deficient species with no information on molecular regulation governing the wood phenotypes. Hence, with the aim to identify the lignin biosynthetic pathway transcripts, transcriptome sequencing of pooled developing secondary wood tissues of a 22-month-old tree was conducted. The processed reads were de novo assembled and 48,493 unigenes were annotated. Quantitative real time PCR was conducted in six even-aged trees to document the natural expression profiles of nine major transcripts from the monolignol pathway. Significant differential expression of Phenylalanine ammonia-lyase (AePAL), Cinnamate 4-hydroxylase (AeC4H), Cinnamyl-alcohol dehydrogenase (AeCAD), Laccase (AeLACI) and Caffeic Acid 3-O-Methyl Transferase (AeCOMT) was documented across all genotypes studied. Transcriptome-wise microsatellites were also mined and is the first co-dominant marker resource in this species. The genomic resource generated in A. excelsa will facilitate understanding the molecular mechanisms of wood formation and accelerate trait-based breeding program through diversity assessment, population structure analysis, clonal discrimination and marker assisted selection.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9

Similar content being viewed by others

References

  • Aldrich PR, Briguglio JS, Kapadia SN, Morker MU, Rawal A, Kalra P, Huebner CD and Greer GK 2010 Genetic structure of the invasive tree Ailanthus altissima in eastern United States cities. J. Bot.

    Article  Google Scholar 

  • Andersen CL, Jensen JL and Orntoft TF 2004 Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 64 5245–5250

    CAS  PubMed  Google Scholar 

  • Auer PL and Doerge RW 2010 Statistical design and analysis of RNA sequencing data. Genetics 185 405–416

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bano S, Ansari S, Choudhary M and Tomar UK 2020 Gender-based genetic variability of Ailanthus excelsa Roxb, populations using, RAPD, ISSR and SCoT Markers. Curr. J. Appl. Sci. Technol. 39 75–83

    Google Scholar 

  • Barros E, Staden CA and Lezar S 2009 A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis. BMC Biotechnol. 9 1472–6750

    Google Scholar 

  • Bhaskaran E 2018 The performance of match producers industrial cooperative societies in Tamil Nadu. https://doi.org/10.13140/RG.2.2.32037.35049

  • Bonawitz ND and Chapple C 2010 The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu. Rev. Genet. 44 337–363

    CAS  PubMed  Google Scholar 

  • Chang P, Zhu L, Zhao M, Li C, Zhang Y and Li L 2019 The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development. Biotechnol. Biotechnol. Equip. 33 967–973

    CAS  Google Scholar 

  • Chen J, Chen B and Zhang D 2015 Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq. BMC Genomics 16 164

    PubMed  PubMed Central  Google Scholar 

  • Chen TW, Gan RC, Fang YK, Chien KY, Lioa WC, et al. 2017 FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci. Rep. 7 10430

    PubMed  PubMed Central  Google Scholar 

  • Dai X, Sinharoy S, Udvardi M and Zhao P 2013 PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinformatics 14 321

    PubMed  PubMed Central  Google Scholar 

  • Dallas JF, Leitch MJB and Hulme HP 2005 Microsatellites for tree of heaven (Ailanthus altissima). Mol. Ecol. Notes 5 340–342

    CAS  Google Scholar 

  • Dharanishanthi V and Dasgupta MG 2016 Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. Mol. Biol. Rep. 43 1129–1146

    CAS  PubMed  Google Scholar 

  • Dharanishanthi V and Ghosh Dasgupta M 2018a Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis. 3 Biotech. 8 315

    PubMed  PubMed Central  Google Scholar 

  • Dharanishanthi V and Ghosh Dasgupta M 2018b Co-expression network of secondary cell wall biogenesis genes in Eucalyptus tereticornis. Silvae Genetica 67 72–78

    Google Scholar 

  • Dhiman RC and Dhiman D 2015 Quantification of wood wastage in mechanized match manufacturing. Int. J. Eng. Res. 3 51–57

    Google Scholar 

  • Elbadawi M, Osman Z, Paridah T, Nasroun T and Kantiner W 2015 Mechanical and physical properties of particleboards made from Ailanthus wood and UF resin fortified by Acacias tannins blend. J. Mater. Environ. Sci. 6 1016–1021

    CAS  Google Scholar 

  • Elzaki OT and Khider TO 2013 Strength Properties of Ailanthus excelsa Roxb. (Tree of Heaven) from Western Sudan. J. Appl. Ind. Sci. 1 38–40

    Google Scholar 

  • Grabber JH 2005 How do lignin composition, structure and cross-linking affect degradability? Crop Sci. 45 820–831

    CAS  Google Scholar 

  • Hansen KD, Wu Z, Irizarry RA and Leek JT 2011 Sequencing technology does not eliminate biological variability. Nat. Biotechnol. 29 572–573

    CAS  PubMed  PubMed Central  Google Scholar 

  • He S, Xie Y, Sun X, et al. 2020 Comparative transcriptome analyses reveal candidate genes regulating wood quality in Japanese larch (Larix kaempferi). J. for. Res. 31 65–73

    CAS  Google Scholar 

  • Jat HS, Singh RK and Mann JS 2011 Ardu (Ailanthus sp) in arid ecosystem: A compatible species for combating with drought and securing livelihood security of resource poor people. Indian J. Tradit. Knowl. 10 102–113

    Google Scholar 

  • Kanberga-Siliņa K, Jansons A and Ruņģis D 2015 Expression of three phenylpropanoid pathway genes in Scots pine (Pinus sylvestris L.) in open-pollinated families with differing relative wood densities during early and late wood formation. Silvae Genet. 64 148–159

    Google Scholar 

  • Kanehisa M and Goto S 2000 KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28 27–30

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kanna SU, Krishnakumar N, Jailani Kather K and MDMA, 2019 Specific gravity and shrinkage of Ailanthus excelsa wood at different age gradations. Int. J. Chem. Stud. 7 3316–3319

    CAS  Google Scholar 

  • Kemena C, Dohmen E and Bornberg-Bauer E 2019 DOGMA: a web server for proteome and transcriptome quality assessment. Nucleic Acids Res. 47 W507–W510

    CAS  PubMed  PubMed Central  Google Scholar 

  • Khan AR, Pervez MT, Babar ME, Naveed N and Shoaib M 2018 A comprehensive study of de novo genome assemblers: current challenges and future prospective. Evol. Bioinform. Online 14 1176934318758650

    PubMed  PubMed Central  Google Scholar 

  • Kumar D, Bhat ZA, Singh P, Shah MY and Bhujbal SS 2010 Ailanthus excelsa Roxb. is really a plant of heaven. Int. J. Pharmacol. 6 535–550

    CAS  Google Scholar 

  • Kumar D, Bhat ZA, Singh P, Khatanglakar V and Bhujbal SS 2011 Antiasthmatic and antiallergic potential of methanolic extract of leaves of Ailanthus excelsa. Rev Bras Farmacogn. 21 139–145

    CAS  Google Scholar 

  • Kurokochi H, Saito Y and Ide Y 2014 Genetic structure of the introduced heaven tree (Ailanthus altissima) in Japan: evidence for two distinct origins with limited admixture. Botany 93 133–139

    Google Scholar 

  • Lavhale MS and Mishra SH 2007 Nutritional and therapeutic potential of Ailanthus excelsa - A Review. Pharmacogn. Rev. 1 105–113

    CAS  Google Scholar 

  • Lavhale MS, Kumar S, Mishra SH and Sitasawad SL 2009 A Novel triterpenoid isolated from the root bark of Ailanthus excelsa Roxb (Tree of Heaven), AECHL-1 as a potential anti-cancer agent. PLoS ONE 4 e5365

    PubMed  PubMed Central  Google Scholar 

  • Li WF, Yang WH, Zhang SG, Han SY and Qi LW 2017 Transcriptome analysis provides insights into wood formation during larch tree aging. Tree Genet. Genomes 13 19

    Google Scholar 

  • Liu Y, Zhou J and White KP 2014 RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30 301–304

    CAS  PubMed  Google Scholar 

  • Livak KJ and Schmittgen TD 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCT method. Methods 25 402–408

    CAS  PubMed  Google Scholar 

  • Ma Q, Bu D, Zhang J, Wu Y and Pei D 2019 The Transcriptome landscape of walnut interspecies hybrid (Juglans hindsii × Juglans regia) and regulation of cambial activity in relation to grafting. Front. Genet. 10 577

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mizrachi E, Hefer CA, Ranik M, Joubert F and Myburg AA 2010 De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 11 681

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mottiar Y, Vanholme R, Boerjan W, Ralph J and Mansfield SD 2016 Designer lignins: harnessing the plasticity of lignification. Curr. Opin. Biotechnol. 37 190–200

    CAS  PubMed  Google Scholar 

  • Nakahama K, Urata N, Shinya T, Hayashi K, Nanto K, Rosa AC and Kawaoka A 2018 RNA-seq analysis of lignocellulose-related genes in hybrid Eucalyptus with contrasting wood basic density. BMC Plant Biol. 18 156

    PubMed  PubMed Central  Google Scholar 

  • Neophytou C, Torutaeva E, Winter S, Meimberg H, Hasenauer H and Curto M 2018 Analysis of microsatellite loci in tree of heaven (Ailanthus altissima (Mill.) Swingle) using SSR-GBS. Tree Genet. Genomes 14 82

    Google Scholar 

  • Neophytou C, Pötzelsberger E, Curto M, Meimberg H and Hasenauer H 2019 Population bottlenecks have shaped the genetic variation of Ailanthus altissima (Mill.) Swingle in an area of early introduction. Forestry Int. J. Forest Res. cpz019 https://doi.org/10.1093/forestry/cpz019

  • Nishimura O, Hara Y and Kuraku S 2017 gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33 3635–3637

    CAS  PubMed  PubMed Central  Google Scholar 

  • Orwa C, Mutua A, Kindt R, Jamnadass R and Simons A 2009 Agroforestree database: a tree reference and selection guide version 4.0 (Nairobi, KE: World Agroforestry Centre ICRAF)

    Google Scholar 

  • Palle SR, Seeve CM, Eckert AJ, Cumbie WP, Goldfarb B and Loopstra CA 2011 Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.). Tree Genet. Genomes 7 193–206

    Google Scholar 

  • Paux E, Tamasloukht M, Ladouce N, Sivadon P and Pettenati JG 2004 Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol. Biol. 55 263–280

    CAS  PubMed  Google Scholar 

  • Peirson SN, Butler JN and Foster RG 2003 Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res. 31 e73

    PubMed  PubMed Central  Google Scholar 

  • Pfaffl MW, Tichopad A, Prgomet C and Neuvians TP 2004 Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper –Excel-based tool using pair-wise correlations. Biotechnol Lett. 26 509–515

    CAS  PubMed  Google Scholar 

  • Plomion C, Leprovost G and Stokes A 2001 Wood formation in trees. Plant Physiol. 127 1513–1523

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rajasugunasekar D, Menason E, Geetha M and Shanthi A 2012 Randomly amplified polymorphic DNA (RAPD) marker analysis in Ailanthus excelsa. Cibtech J. Biotechnol. 1 32–37

    Google Scholar 

  • Ramanathan D 2015 Match wood production through agroforestry issues and constraints (CA, USA: Lap Lambert Academic Publishing)

    Google Scholar 

  • Rastogi S and Dwivedi UN 2008 Manipulation of lignin in plants with special reference to O-methyltransferase. Plant Sci. 174 264–277

    CAS  Google Scholar 

  • Shinya T, Iwata E, Nakahama K, Fukuda Y, Hayashi K, Nanto K, Rosa AC and Kawaoka A 2016 Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition. Front. Plant Sci. 7 443

    PubMed  PubMed Central  Google Scholar 

  • Sumathi R, Rajasugunasekar D, Brindha B, Lakshmidevi R, Suresh Babu D, Senthilkumar N and Murugesan S 2017 Ailanthus excelsa Roxb. (Simaroubaceae) leaf: as a potential fodder additive. World J. Res. Rev. 5 1–5

    Google Scholar 

  • Thavamanikumar S, McManus LJ, Ades PK, Bossinger G, Stackpole DJ, Kerr R, Hadjigol S, Freeman JS, Vaillancourt RE, Zhu P and Tibbits JF 2014 Association mapping for wood quality and growth traits in Eucalyptus globulus ssp. globulus Labill identifies nine stable marker-trait associations for seven traits. Tree Genet. Genomes 10 1661–1678

    Google Scholar 

  • Tumenjargal B, Ishiguri F, Aiso H, et al. 2020 Physical and mechanical properties of wood and their geographic variations in Larix sibirica trees naturally grown in Mongolia. Sci. Rep. 10 12936

    CAS  PubMed  PubMed Central  Google Scholar 

  • Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. 2007 Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35 W71–W74

    PubMed  PubMed Central  Google Scholar 

  • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A and Speleman F 2002 Accurate normalisation of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3 1–11

    Google Scholar 

  • Wang C, Zhang N, Gao C, Cui Z, Sun D, Yang C and Wang Y 2014 Comprehensive transcriptome analysis of developing xylem responding to artificial bending and gravitational stimuli in Betula platyphylla. PLoS ONE 9 e87566

    PubMed  PubMed Central  Google Scholar 

  • Xie F, Xiao P, Chen D, Xu L and Zhang B 2012 miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol. 80 75–84

    CAS  Google Scholar 

  • Xie M, Zhang J, Tschaplinski TJ, Tuskan GA, Chen J-G and Muchero W 2018 Regulation of lignin biosynthesis and its role in growth-defense tradeoffs. Front. Plant Sci. 9 1427

    PubMed  PubMed Central  Google Scholar 

  • Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q and Wang Y 2019 OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 47 W52–W58

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang SH and Loopstra CA 2005 Seasonal variation in gene expression for loblolly pines (Pinus taeda) from different geographical regions. Tree Physiol. 25 1063–1073

    CAS  PubMed  Google Scholar 

  • Zhang Y, Han X, Sang J, He X, Liu M, Qiao G, Zhuo R, He G and Hu J 2016 Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PeerJ 4 e2097

    PubMed  PubMed Central  Google Scholar 

  • Zhong R, Cui D and Ye ZH 2019 Secondary cell wall biosynthesis. New Phytol. 221 1703–1723

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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

Accession Number

The sequence data has been deposited in NCBI’s Short Read Archive with the accession number PRJNA563787.

Author information

Authors and Affiliations

  1. Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641 002, India

    Modhumita Ghosh Dasgupta, A Muneera Parveen & D Rajasugunasekar

  2. Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500 007, India

    Kandasamy Ulaganathan

Authors
  1. Modhumita Ghosh Dasgupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A Muneera Parveen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D Rajasugunasekar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kandasamy Ulaganathan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Modhumita Ghosh Dasgupta.

Additional information

Communicated by Ashis Kumar Nandi.

Corresponding editor: Ashis Kumar Nandi

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dasgupta, M.G., Parveen, A.M., Rajasugunasekar, D. et al. Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts in Ailanthus excelsa Roxb., a multi-purpose tropical tree species. J Biosci 46, 105 (2021). https://doi.org/10.1007/s12038-021-00218-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12038-021-00218-7

Keywords

Search

Navigation