Genome-wide analysis of the lignin toolbox of Eucalyptus grandis

dc.contributor.authorCarocha, Victor
dc.contributor.authorSoler, Marçal
dc.contributor.authorHefer, Charles
dc.contributor.authorCassan-Wang, Hua
dc.contributor.authorFevereiro, Pedro
dc.contributor.authorMyburg, Alexander Andrew
dc.contributor.authorPaiva, Jorge A.P.
dc.contributor.authorGrima-Pettenati, Jacqueline
dc.date.accessioned2016-08-30T13:35:19Z
dc.date.available2016-08-30T13:35:19Z
dc.date.issued2015-06
dc.description.abstractLignin, a major component of secondary cell walls, hinders the optimal processing of wood for industrial uses. The recent availability of the Eucalyptus grandis genome sequence allows comprehensive analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway and identification of those mainly involved in xylem developmental lignification. We performed genome-wide identification of putative members of the lignin gene families, followed by comparative phylogenetic studies focusing on bona fide clades inferred from genes functionally characterized in other species. RNA-seq and microfluid real-time quantitative PCR (RT-qPCR) expression data were used to investigate the developmental and environmental responsive expression patterns of the genes. The phylogenetic analysis revealed that 38 E. grandis genes are located in bona fide lignification clades. Four multigene families (shikimate O-hydroxycinnamoyltransferase (HCT), p-coumarate 3-hydroxylase (C3H), caffeate/5-hydroxyferulate O-methyltransferase (COMT) and phenylalanine ammonia-lyase (PAL)) are expanded by tandem gene duplication compared with other plant species. Seventeen of the 38 genes exhibited strong, preferential expression in highly lignified tissues, probably representing the E. grandis core lignification toolbox. The identification of major genes involved in lignin biosynthesis in E. grandis, the most widely planted hardwood crop world-wide, provides the foundation for the development of biotechnology approaches to develop tree varieties with enhanced processing qualities.en_ZA
dc.description.departmentGeneticsen_ZA
dc.description.librarianhb2016en_ZA
dc.description.sponsorshipThis work, part of the LABEX project TULIP (ANR-10-LABX-41), was supported by grants from the Project Tree For Joules (ANR-2010-KBBE-007-01 and FCT-PKBBE/ AGR_GPL/0001/2010), the CNRS, the Toulouse III University (UPS), and the FCT project microEGo (PTDC/AGR-GPL/098179/2008). V.C. was supported by a FCT PhD grant (SFRH/BD/72982/2010). M.S. received a postdoctoral fellowship ‘Beatriu de Pinós’ from the DURSI de la Generalitat de Catalunya. J.A.P.P. acknowledges FCT for the research contract Ciência 2008 program and the postdoctoral fellowship SFRH/BPD/92207/2013. We are grateful to C. Araujo and L. Neves (Altri Florestal, Portugal), C. Marques (RAIZ, Portugal) and L. Harvengt (FCBA, France) for kindly providing and/or allowing collection of Eucalyptus samples, and C. Graça (IBET, IICT), N. Saidi, H. Yu and E. Camargo (all LRSV) for help with sample design/collection and RNA extraction. We also thank N. Ladouce (LRSV) and the Genotoul Genomic platform http://get.genotoul.fr/ for technical assistance with the Biomark Fluidigm RT-qPCR amplifications, and E. Mizrachi for assistance with RNA-seq data analysis. RNA-seq was funded by Mondi and Sappi through the FMG Program, the THRIP Program (UID 80118), the NRF (UID 71255 and 86936) and the DST of South Africa.en_ZA
dc.description.urihttp://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-8137en_ZA
dc.identifier.citationCarocha, V, Soler, M, Hefer, C, Cassan-Wang, H, Fevereiro, P, Myburg, AA, Paiva, JAP & Grima-Pettenati, J 2015, 'Genome-wide analysis of the lignin toolbox of Eucalyptus grandis', New Phytologist, vol. 206, no. 4, pp. 1297-1313.en_ZA
dc.identifier.issn0028-646X (print)
dc.identifier.issn1469-8137 (online)
dc.identifier.other10.1111/nph.13313
dc.identifier.urihttp://hdl.handle.net/2263/56496
dc.language.isoenen_ZA
dc.publisherWileyen_ZA
dc.rights© 2015 The Authors New Phytologist © 2015 New Phytologist Trust. This is the pre-peer reviewed version of the following article : Genome-wide analysis of the lignin toolbox of Eucalyptus grandis, New Phytologist, vol. 206, no. 4, pp. 1297-1313, 2015. doi : 10.1111/nph.13313. The definite version is available at : http://onlinelibrary.wiley.comjournal/10.1111/(ISSN)1469-8137.en_ZA
dc.subjectEucalyptusen_ZA
dc.subjectLignin biosynthesisen_ZA
dc.subjectPhenylpropanoid pathwayen_ZA
dc.subjectSecondary cell wall (SCW)en_ZA
dc.subjectXylemen_ZA
dc.titleGenome-wide analysis of the lignin toolbox of Eucalyptus grandisen_ZA
dc.typePostprint Articleen_ZA

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