title: The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.
abstract: The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Marçal
authors.initials: M
authors.lastname: Soler
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Eduardo Leal Oliveira
authors.initials: EL
authors.lastname: Camargo
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.|Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.|Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal.
authors.forename: Victor
authors.initials: V
authors.lastname: Carocha
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Hua
authors.initials: H
authors.lastname: Cassan-Wang
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: San Clemente
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Savelli
authors.affiliation: Bioinformatics and Computational Biology Unit, Department of Biochemistry, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Hefer
authors.affiliation: Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal.|Instituto de Investigaçao Científica e Tropical (IICT/MNE) Palacio Burnay - Rua da Junqueira, 30, 1349-007, Lisboa, Portugal.
authors.forename: Jorge A Pinto
authors.initials: JA
authors.lastname: Paiva
authors.affiliation: 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.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Grima-Pettenati
mesh_terms: D005075:Biological Evolution; D003198:Computer Simulation; D005052:Eucalyptus / Q000235:genetics* / Q000254:growth & development*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D044085:Microfluidics; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014934:Wood / Q000254:growth & development*
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D014157:Transcription Factors
keywords: Eucalyptus grandis; R2R3-MYB transcription factors; cambium; evolution; secondary growth; tandem duplications; wood formation