Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae.

Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.

The Dynamics of Flower Development in Castanea sativa Mill.

The sweet chestnut tree (Castanea sativa Mill.) is one of the most significant Mediterranean tree species, being an important natural resource for the wood and fruit industries. It is a monoecious species, presenting unisexual male catkins and bisexual catkins, with the latter having distinct male and female flowers. Despite the importance of the sweet chestnut tree, little is known regarding the molecular mechanisms involved in the determination of sexual organ identity. Thus, the study of how the different flowers of C. sativa develop is fundamental to understand the reproductive success of this species and the impact of flower phenology on its productivity. In this study, a C. sativa de novo transcriptome was assembled and the homologous genes to those of the ABCDE model for floral organ identity were identified. Expression analysis showed that the C. sativa B- and C-class genes are differentially expressed in the male flowers and female flowers. Yeast two-hybrid analysis also suggested that changes in the canonical ABCDE protein-protein interactions may underlie the mechanisms necessary to the development of separate male and female flowers, as reported for the monoecious Fagaceae Quercus suber. The results here depicted constitute a step towards the understanding of the molecular mechanisms involved in unisexual flower development in C. sativa, also suggesting that the ABCDE model for flower organ identity may be molecularly conserved in the predominantly monoecious Fagaceae family.

Unisexual flower initiation in the monoecious Quercus suber L.: a molecular approach.

Several plant species display a temporal separation of the male and female flower organ development to enhance outbreeding; however, little is known regarding the genetic mechanisms controlling this temporal separation. Quercus suber is a monoecious oak tree with accentuated protandry: in late winter, unisexual male flowers emerge adjacent to the swollen buds, whereas unisexual female flowers emerge in the axils of newly formed leaves formed during spring (4-8 weeks after male flowering). Here, a phylogenetic profiling has led to the identification of cork oak homologs of key floral regulatory genes. The role of these cork oak homologs during flower development was identified with functional studies in Arabidopsis thaliana. The expression profile throughout the year of flower regulators (inducers and repressors), in leaves and buds, suggests that the development of male and female flowers may be preceded by separated induction events. Female flowers are most likely induced during the vegetative flush occurring in spring, whereas male flowers may be induced in early summer. Male flowers stay enclosed within the pre-dormant buds, but complete their development before the vegetative flush of the following year, displaying a long period of anthesis that spans the dormant period. Our results portray a genetic mechanism that may explain similar reproductive habits in other monoecious tree species.