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Pathways associated with lignin biosynthesis in lignomaniac jute fibres

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Abstract

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136  bp, respectively, were assembled de novo, ~77–79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37–40 %) and GO (~22–28 %) classifications and mapped to 189 KEGG pathways (~19–21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers’ deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.

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References

  • Achnine L, Blancaflor EB, Rasmussen S, Dixon RA (2004) Colocalization of l-phenylalanine ammonia-lyase and cinnamate 4-hydroxylase for metabolic channeling in phenylpropanoid biosynthesis. Plant Cell 16:3098–3109

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of Kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7:e52443

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anterola AM, Lewis NG (2002) Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61:221–294

    Article  CAS  PubMed  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo S, Van Deynze A (2012) De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs SSRs and candidate genes. BMC Genomics 13:571

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Besseau S, Hoffmann L, Geoffroy P, Lapierre C, Pollet B, Legrand M (2007) Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell 19:148–162

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bouvier d’Yvoire M, Bouchabke-Coussa O, Voorend W, Antelme S, Cézard L, Legée F, Lebris P, Legay S, Whitehead C, McQueen-Mason SJ, Gomez LD, Jouanin L, Lapierre C, Sibout R (2013) Disrupting the cinnamyl alcohol dehydrogenase 1 gene (BdCAD1) leads to altered lignification and improved saccharification in Brachypodium distachyon. Plant J 73:496–508

    Article  PubMed  Google Scholar 

  • Chai G, Hu R, Zhang D, Qi G, Zuo R, Cao Y, Chen P, Kong Y, Zhou G (2012) Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC Genomics 13:253

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chapple CCS, Vogt T, Ellis BE, Somerville CR (1992) An Arabidopsis mutant defective in the general phenylpropanoid pathway. Plant Cell 4:1413–1424

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chiaiese P, Ruotolo G, Di Matteo A, De Santo Virzo A, De Marco A, Filippone E (2011) Cloning and expression analysis of kenaf (Hibiscus cannabinus L.) major lignin and cellulose biosynthesis gene sequences and polymer quantification during plant development. Ind Crops Prod 34:1072–1078

    Article  CAS  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • De Pauw MA, Vidmar JJ, Collins J, Bennett RA, Deyholos MK (2007) Microarray analysis of bast fibre producing tissues of Cannabis sativa identifies transcripts associated with conserved and specialised processes of secondary wall development. Func Plant Biol 34:737–749

    Article  Google Scholar 

  • Del Rio JC, Rencoret J, Matques G, Li J, Gellerstedt G, Jiménez-Barbero J, Martínez AT, Gutiérrez A (2009) Structural characterization of the lignin from jute (Corchorus capsularis) fibers. J Agric Food Chem 57:10271–10281

    Article  PubMed  Google Scholar 

  • Duan J, Xia C, Zhao G, Jia J, Kong X (2012) Optimizing de novo common wheat transcriptome assembly using short-read RNA-seq data. BMC Genomics 13:392

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Feldmeyer B, Wheat C, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12:317

    Article  PubMed Central  PubMed  Google Scholar 

  • Fenart S, Ndong Y-P, Duarte J, Riviere N, Wilmer J, van Wuytswinkel O, Lucau A, Cariou E, Neutelings G, Gutierrez L, Chabbert B, Guillot X, Tavernier R, Hawkins S, Thomasset B (2010) Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. BMC Genomics 11:592

    Article  PubMed Central  PubMed  Google Scholar 

  • Fornalé S, Capellades M, Encina A, Wang K, Irar S, Lapierre C, Ruel K, Joseleau J-P, Berenguer J, Puigdomènech P, Rigau J, Caparrós-Ruiz D (2012) Altered lignin biosynthesis improves cellulosic bioethanol production in transgenic maize plants down-regulated for cinnamyl alcohol dehydrogenase. Mol Plant 5:817–830

    Article  PubMed  Google Scholar 

  • Fu C, Xiao X, Xi Y, Ge Y, Chen F, Bouton J, Dixon RA, Wang Z-Y (2011) Downregulation of cinnamyl alcohol dehydrogenase (CAD) leads to improved saccharification efficiency in switchgrass. Bioenerg Res 4:153–164

    Article  Google Scholar 

  • Gallego-Giraldo L, Escamilla-Trevino L, Jackson LA, Dixon RA (2011) Salicylic acid mediates the reduced growth of lignin down-regulated plants. Proc Natl Acad Sci USA 108:20814–20819

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26:2731–2744

    Article  CAS  PubMed  Google Scholar 

  • Gorshkova T, Brutch N, Chabbert B, Deyholos M, Hayashi T, Lev-Yadun S, Mellerowicz EJ, Morvan C, Neutelings G, Pilate G (2012) Plant fibre formation: state of the art, recent and expected progress, and open questions. Crit Rev Plant Sci 31:201–228

    Article  CAS  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hao Z, Mohnen D (2014) A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes. Crit Rev Biochem Mol Biol 49:212–241

    Article  CAS  PubMed  Google Scholar 

  • Hao DC, Ge G, Xiao P, Zhang Y, Yang L (2011) The first insight into the tissue specific Taxus transcriptome via Illumina second generation sequencing. PLoS One 6:e21220

    Article  CAS  PubMed Central  Google Scholar 

  • Hobson N, Roach MJ, Deyholos MK (2010) Gene expression in tension wood and bast fibres. Russ J Plant Physiol 57:321–327

    Article  CAS  Google Scholar 

  • Hoffmann L, Besseau S, Geoffroy P, Ritzenthaler C, Meyer D, Lapierre C, Pollet B, Legrand M (2004) Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase affects phenylpropanoid biosynthesis. Plant Cell 16:1446–1465

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hu W-J, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Tsai C-J, Chiang VL (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat Biotechnol 17:808–812

    Article  CAS  PubMed  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Lengauer T, Schneider R, Bork P et al (eds) Proceedings of the seventh international conference on intelligent systems for molecular biology. AAAI Press, Palo Alto, pp 138–158

    Google Scholar 

  • Johnson KL, Jones BJ, Bacic A, Schultz CJ (2003) The fasciclin-like arabinogalactan proteins of Arabidopsis. A multigene family of putative cell adhesion molecules. Plant Physiol 133:1911–1925

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kalra S, Puniya BL, Kulshreshtha D, Kumar S, Kaur J, Ramachandran S, Singh K (2013) De novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant Chlorophytum borivilianum. PLoS One 8:e83336

    Article  PubMed Central  PubMed  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109–D114

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kawaoka A, Kaothien P, Yoshida K, Endo S, Yamada K, Ebinuma H (2000) Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. Plant J 22:289–301

    Article  CAS  PubMed  Google Scholar 

  • Koziel SP (2010) Genetic analysis of lignification and secondary wall development in bast fibres of hemp (Cannabis sativa). Dissertation, University of Alberta

  • Kundu A, Sarkar D, Mandal NA, Sinha MK, Mahapatra BS (2012) A secondary phloic (bast) fibre-shy (bfs) mutant of dark jute (Corchorus olitorius L.) develops lignified fibre cells but is defective in cambial activity. Plant Growth Regul 67:45–55

    Article  CAS  Google Scholar 

  • Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinform 32: 11

  • Lee Y, Chen F, Gallego-Giraldo L, Dixon RA, Voit EO (2011) Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis. PLoS Comput Biol 7:e1002047

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lev-Yadun S (2010) Plant fibres: initiation, growth, model plants and open questions. Russ J Plant Physiol 57:305–315

    Article  CAS  Google Scholar 

  • Li L, Cheng XF, Leshkevich J, Umezawa T, Harding SA, Chiang VL (2001) The last step of syringyl monolignol biosynthesis in angiosperms is regulated by a novel gene encoding sinapyl alcohol dehydrogenase. Plant Cell 13:1567–1586

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967

    Article  CAS  PubMed  Google Scholar 

  • Li D, Deng Z, Qin B, Liu X, Men Z (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu S, Li W, Wu Y, Chen C, Lei J (2013a) De novo transcriptome assembly in chilli pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of Capsaicinoids. PLoS One 8:e48156

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu T, Zhu S, Tang Q, Chen P, Yu Y, Tang S (2013b) De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). BMC Genomics 14:125

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Long S-H, Deng X, Wang Y-F, Li X, Qiao R-Q, Qiu C-S, Guo Y, Hao D-M, Jia W-Q, Chen X-B (2012) Analysis of 2,297 expressed sequence tags (ESTs) from a cDNA library of flax (Linum ustitatissimum L.) bark tissue. Mol Biol Rep 39:6289–6296

    Article  CAS  PubMed  Google Scholar 

  • Lulin H, Xiao Y, Pei S, Wen T, Shangqin H (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 7:e38653

    Article  PubMed Central  PubMed  Google Scholar 

  • Maeda H, Dudareva N (2012) The shikimate pathway and aromatic amino acid biosynthesis in plants. Annu Rev Plant Biol 63:73–105

    Article  CAS  PubMed  Google Scholar 

  • Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

    Article  CAS  PubMed  Google Scholar 

  • Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682

    Article  CAS  PubMed  Google Scholar 

  • Martin L, Fei Z, Giovannoni J, Rose JKC (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:66

    Article  PubMed Central  PubMed  Google Scholar 

  • Meshram JH, Palit P (2013) On the role of cell wall lignin in determining the fineness of jute fibre. Acta Physiol Plant 35:1565–1578

    Article  CAS  Google Scholar 

  • Mikshina P, Chernova T, Chemikosova S, Ibragimova N, Mokshina N, Gorshkova T (2013) Cellulosic fibers: role of matrix polysaccharides in structure and function. In: van de Ven T, Godbout L (eds) Cellulose- fundamental aspects. InTech, Rijeka, pp 91–112

    Google Scholar 

  • Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB (2013) RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res 23:679–686

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mitchell HJ, Hall JL, Barber MS (1994) Elicitor-induced cinnamyl alcohol dehydrogenase activity in lignifying wheat (Triticum aestivum L.) leaves. Plant Physiol 104:551–556

    CAS  PubMed Central  PubMed  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185

    Article  PubMed Central  PubMed  Google Scholar 

  • Okonechnikov K, Golosova O, Fursov M, The UGENE team (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167

    Article  CAS  PubMed  Google Scholar 

  • Patten AM, Jourdes M, Brown EE, Laborie M-P, Davin LB, Lewis NG (2007) Reaction tissue formation and stem tensile modulus properties in wild-type and p-coumarate-3-hydroxylase downregulated lines of alfalfa, Medicago sativa (Fabaceae). Am J Bot 94:912–925

    Article  PubMed  Google Scholar 

  • Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LGG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38:D822–D827

    Article  PubMed Central  PubMed  Google Scholar 

  • Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102:8633–8638

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:2002–2007

    Article  Google Scholar 

  • Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30:e36

    Article  PubMed Central  PubMed  Google Scholar 

  • Piskol R, Ramaswami G, Li JB (2013) Reliable identification of genomic variants from RNA-Seq data. Am J Hum Genet 93:641–651

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Preisner M, Kulma A, Zebrowski J, Dyminska L, Hanuza J, Arendt M, Starzycki M, Szopa J (2014) Manipulating cinnamyl alcohol dehydrogenase (CAD) expression in flax affects fibre composition and properties. BMC Plant Biol 14:50

    Article  PubMed Central  PubMed  Google Scholar 

  • Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol 133:1051–1071

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  CAS  PubMed  Google Scholar 

  • Roach M, Deyholos M (2007) Microarray analysis of flax (Linum usitatissimum L.) stems identifies transcripts enriched in fibre-bearing phloem tissues. Mol Genet Genomics 278:149–165

    Article  CAS  PubMed  Google Scholar 

  • Roach MJ, Mokshina NY, Badhan A, Snegireva AV, Hobson N, Deyholos MK, Gorshkova TA (2011) Development of cellulosic secondary walls in flax fibers requires β-galactosidase. Plant Physiol 156:1351–1363

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320–W324

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Saballos A, Ejeta G, Sanchez E, Kang C, Vermerris W (2009) A genomewide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the brown midrib6 gene. Genetics 181:783–795

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sablok G, Fu Y, Bobbio V, Laura M, Rotino GL, Bagnaresi P, Allavena A, Velikova V, Viola R, Loreto F, Li M, Varotto C (2014) Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. Plant Biotechnol J 12:554–567

    Article  CAS  PubMed Central  Google Scholar 

  • Saha P, Datta K, Majumder S, Sarkar C, China SP, Sarkar SN, Sarkar D, Datta SK (2014) Agrobacterium mediated genetic transformation of commercial jute cultivar Corchorus capsularis cv. JRC 321 using shoot tip explants. Plant Cell Tissue Organ Cult 118:313–326

    Article  CAS  Google Scholar 

  • Sarkar D, Sinha MK, Kundu A, Kar CS, Saha A, Kharbikar LL, Mahapatra BS (2010) Why is ramie the strongest yet stiffest of bast fibres? Curr Sci 98:1570–1572

    Google Scholar 

  • Sarkar D, Kundu A, Saha A, Mondal NA, Sinha MK, Mahapatra BS (2011) First nuclear DNA amounts in diploid (2n = 2x = 14) Corchorus spp. by flow cytometry: genome sizes in the cultivated jute species (C. capsularis L. and C. olitorius L.) are ~300 % smaller than the reported estimate of 1100–1350 Mb. Caryologia 64:147–153

    Article  Google Scholar 

  • Sengupta G, Palit P (2004) Characterization of a lignified secondary phloem fibre-deficient mutant of jute (Corchorus capsularis). Ann Bot 93:211–220

    Article  PubMed Central  PubMed  Google Scholar 

  • Shi R, Sun Y-H, Li Q, Heber S, Sederoff R, Chiang VL (2010) Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol 51:144–163

    Article  CAS  PubMed  Google Scholar 

  • Sibout R, Eudes A, Pollet B, Goujon T, Mila I, Granier F, Séguin A, Lapierre C, Jouanin L (2003) Expression pattern of two paralogs encoding cinnamyl alcohol dehydrogenases in Arabidopsis. Isolation and characterization of the corresponding mutants. Plant Physiol 132:848–860

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed Central  PubMed  Google Scholar 

  • The Angiosperm Phylogeny Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105–121

    Article  Google Scholar 

  • Trabucco G, Matos D, Lee S, Saathoff A, Priest H, Mockler T, Sarath G, Hazen S (2013) Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. BMC Biotechnol 13:61

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tzin V, Galili G (2010) The biosynthetic pathways for shikimate and aromatic amino acids in Arabidopsis thaliana. Arabidopsis Book 8:e0132

    Article  PubMed Central  PubMed  Google Scholar 

  • van den Broeck HC, Maliepaard C, Ebskamp MJM, Toonen MAJ, Koops AJ (2008) Differential expression of genes involved in C1 metabolism and lignin biosynthesis in wooden core and bast tissues of fibre hemp (Cannabis sativa L.). Plant Sci 174:205–220

    Article  Google Scholar 

  • Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP et al (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10:347

    Article  PubMed Central  PubMed  Google Scholar 

  • Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11:726

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Y, Chantreau M, Sibout R, Hawkins S (2013) Plant cell wall lignification and monolignol metabolism. Front Plant Sci 4:220

    PubMed Central  PubMed  Google Scholar 

  • Wong MML, Cannon CH, Wickneswari R (2011) Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 12:342

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G et al (2014) SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30:1660–1666

    Article  CAS  PubMed  Google Scholar 

  • Xu Z, Zhang D, Hu J, Zhou X, Ye X, Reichel K, Stewart N, Syrenne R et al (2009) Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinformatics 10:S3

    Article  PubMed Central  PubMed  Google Scholar 

  • Xu D-L, Long H, Liang J-J, Zhang J, Chen X, Li J-L, Pan Z-F, Deng G-B, Yu M-Q (2012) De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics 13:133

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhao Q, Dixon RA (2011) Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant Sci 16:227–233

    Article  CAS  PubMed  Google Scholar 

  • Zou D, Chen X, Zou D (2013) Sequencing, de novo assembly, annotation and SSR and SNP detection of sabaigrass (Eulaliopsis binata) transcriptome. Genomics 102:57–62

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We acknowledge with thanks the Xcelris Labs Limited, Ahmedabad, for assistance with Illumina paired-end sequencing, raw data processing and related bioinformatics analyses. We also thank Dr. Surendra Chikara (Director, Xcelris) for his valuable comments and suggestions during the course of this study. The research was supported by a grant (ICAR/NRCPB/NPTC-3052) from ICAR Network Project of Transgenics in Crops (ICAR-NPTC), Indian Council of Agricultural Research (ICAR), New Delhi. Comments and suggestions on the manuscript from the Editor and two anonymous reviewers are gratefully acknowledged.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The laboratory and green house experiments related directly or indirectly to the subject of this manuscript essentially complied with appropriate ethical standards, according to existing rules and regulations of Indian Council of Agricultural Research (ICAR), Government of India.

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Authors and Affiliations

  1. Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700 120, West Bengal, India

    Avrajit Chakraborty, Debabrata Sarkar, Pratik Satya & Pran Gobinda Karmakar

  2. ICAR-National Research Centre on Plant Biotechnology (NRCPB), Pusa Campus, New Delhi, 110 012, India

    Nagendra Kumar Singh

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  1. Avrajit Chakraborty
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  2. Debabrata Sarkar
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  3. Pratik Satya
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  4. Pran Gobinda Karmakar
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  5. Nagendra Kumar Singh
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Corresponding author

Correspondence to Debabrata Sarkar.

Additional information

Communicated by S. Hohmann.

The Illumina paired-end sequence data have been deposited at the NCBI Sequence Read Archive (SRA) under the accession SRP047473 vide BioProject PRJNA255934 and BioSamples SAMN02934031 and SAMN02934032. The Transcriptome Shotgun Assembly (TSA) projects have been deposited at DDBJ/EMBL/GenBank under the accessions GBSD00000000 and GBSE00000000. The versions described in this paper are the first versions, GBSD01000000 and GBSE01000000.

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Chakraborty, A., Sarkar, D., Satya, P. et al. Pathways associated with lignin biosynthesis in lignomaniac jute fibres. Mol Genet Genomics 290, 1523–1542 (2015). https://doi.org/10.1007/s00438-015-1013-y

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