title: Genome-wide analysis of the lignin toolbox of Eucalyptus grandis.
abstract: Lignin, 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.
authors: LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France.|Instituto de Tecnologia de Química Biológica (ITQB), Biotecnologia de Células Vegetais, Av. da República, 2781-157, Oeiras, Portugal.|Instituto de Investigação Científica e Tropical (IICT/MNE), Palácio Burnay, Rua da Junqueira, 30, 1349-007, Lisboa, Portugal.
authors: Victor
authors: V
authors: Carocha
authors: LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors: Marçal
authors: M
authors: Soler
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.|Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, South Africa.
authors: Charles
authors: C
authors: Hefer
authors: LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors: Hua
authors: H
authors: Cassan-Wang
authors: Instituto de Tecnologia de Química Biológica (ITQB), Biotecnologia de Células Vegetais, Av. da República, 2781-157, Oeiras, Portugal.|Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Campo Grande, 1749-016, Lisboa, Portugal.
authors: Pedro
authors: P
authors: Fevereiro
authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.|Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
authors: Alexander A
authors: AA
authors: Myburg
authors: Instituto de Investigação Científica e Tropical (IICT/MNE), Palácio Burnay, Rua da Junqueira, 30, 1349-007, Lisboa, Portugal.|iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
authors: Jorge A P
authors: JA
authors: Paiva
authors: LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors: Jacqueline
authors: J
authors: Grima-Pettenati
mesh_terms: D003198:Computer Simulation; D004777:Environment; D005052:Eucalyptus / Q000201:enzymology / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D006900:Hydroxylation; D008031:Lignin / Q000378:metabolism*; D008745:Methylation; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics; D010802:Phylogeny; D020005:Propanols / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
chemical_list: D020005:Propanols; C439395:1-phenylpropanol; D008031:Lignin; D010650:Phenylalanine Ammonia-Lyase
keywords: Eucalyptus; lignin biosynthesis; phenylpropanoid pathway; secondary cell wall; xylem