The Eucalyptus grandis R2R3‐MYB transcription factor family: evidence for woody growth‐related evolution and function

Abstract

SummaryThe 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.

Genome-wide analysis of the MYB gene family in physic nut ( Jatropha curcas L.)

“…The uncompressed tree is available in Supplementary Fig. S4. (shown in brackets) were coincident with the previous report (Soler et al, 2014). Eucalyptus lacks clades of C12, C18, C22 and C24 (Supplementary Fig.…”

“…The topologies on the phylogenetic trees are similar to previously reported phylogenetic analyses, given the comparisons with genes from rice and Arabidopsis on each clade. According to our results, and based on previous analyses of the grape, eucalyptus, Arabidopsis and rice MYB gene families (Stracke et al, 2001;Dubos et al, 2010;Soler et al, 2014), these MYB proteins could be classified into 45 clades, C1 to C45 ( Supplementary Fig. S4, Fig.…”

“…2). They are classed into the five woody-preferential R2R3-MYB subgroups (Soler et al, 2014) based on the phylogenetic analysis of the R2R3-MYB proteins from physic nut, Arabidopsis, grape, and eucalyptus ( Supplementary Fig. S5).…”

“…Japonica) were obtained from the plant transcription factor database website (http://plntfdb.bio.unipotsdam.de/v3.0/). The castor bean (Supplementary Table S1), Physcomitrella patens, Eucalyptus grandis, Vitis vinifera, and green algae MYB gene sequences were downloaded from Phytozome (http://www.phytozome.net; Chan et al, 2010;Soler et al, 2014). The tree was constructed using the neighbor-joining (NJ) method and 1000 bootstraps to arrange putative full-length MYB amino acid sequences with software ClustalX (1.83), and the results were displayed with Mega software version 4 (Tamura et al, 2007).…”

“…The full-length amino acid sequences of MYB proteins were aligned using CLUSTAL_X and the phylogenetic tree was constructed using the neighbor-joining method. The bracketed subgroups were previously classified by Soler et al (2014). Subgroup names are included next to each clade together with a short name to simplify nomenclature.…”