The MYB transcription factor family is one of the largest gene families playing regulatory roles in plant growth and development. The MYB family has been studied in a variety of plant species but has not been reported in Taxus chinensis. Here we identified 72 putative R2R3-MYB genes in T. chinensis using a comprehensive analysis. Sequence features, conversed domains and motifs were characterized. The phylogenetic analysis showed TcMYBs and AtMYBs were clustered into 36 subgroups, of which 24 subgroups included members from T. chinensis and Arabidopsis thaliana, while 12 subgroups were specific to one species. This suggests the conservation and specificity in structure and function of plant R2R3-MYBs. The expression of TcMYBs in various tissues and different ages of xylem were investigated. Additionally, miRNA-mediated posttranscriptional regulation analysis revealed that TcMYBs were the targets of miR858, miR159 and miR828, suggesting the posttranscriptional regulation of MYBs is highly conserved in plants. The results provide a basis for further study the role of TcMYBs in the regulation of secondary metabolites of T. chinensis.

Soil salinization is a matter of concern worldwide. It can eventually lead to the desertification of land and severely damage local agricultural production and the ecological environment. Betula halophila is a tree with high salt tolerance, so it is of importance to understand and discover the salt responsive genes of B. halophila for breeding salinity resistant varieties of trees. However, there is no report on the transcriptome in response to salt stress in B. halophila. Using Illumina sequencing platform, approximately 460 M raw reads were generated and assembled into 117,091 unigenes. Among these unigenes, 64,551 unigenes (55.12%) were annotated with gene descriptions, while the other 44.88% were unknown. 168 up-regulated genes and 351 down-regulated genes were identified, respectively. These Differentially Expressed Genes (DEGs) involved in multiple pathways including the Salt Overly Sensitive (SOS) pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. The gene ontology (GO) enrichments suggested that the DEGs were mainly involved in a plant-type cell wall organization biological process, cell wall cellular component, and structural constituent of cell wall molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that the top-four enriched pathways were ‘Fatty acid elongation’, ‘Ribosome’, ‘Sphingolipid metabolism’ and ‘Flavonoid biosynthesis’. The expression patterns of sixteen DEGs were analyzed by qRT-PCR to verify the RNA-seq data. Among them, the transcription factor AT-Hook Motif Nuclear Localized gene and dehydrins might play an important role in response to salt stress in B. halophila. Our results provide an important gene resource to breed salt tolerant plants and useful information for further elucidation of the molecular mechanism of salt tolerance in B. halophila.

N⁶-methyladenosine (m⁶A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m⁶A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m⁶A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m⁶A pathway genes in Poplar 84K (Populus alba × Populus glandulosa), including 14 m⁶A writers, 14 m⁶A erasers and 33 m⁶A readers. Phylogenetic analysis indicated that the m⁶A writers and erasers were clustered into four groups and m⁶A readers were clustered into two groups. Promoter analysis showed that m⁶A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m⁶A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15. Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCRshowed that PagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m⁶A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K.

Taxus chinensis is a precious woody species with significant economic value. Anthocyanin as flavonoid derivatives plays a crucial role in plant biology and human health. However, the genes involved in anthocyanin biosynthesis have not been identified in T. chinensis. In this study, twenty-five genes involved in anthocyanin biosynthesis were identified, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, anthocyanidin synthase, flavonoid 3’-hydroxylase, flavonoid 3’,5’-hydroxylase, dihydroflavonol 4-reductase, anthocyanidin reductase, and leucoanthocyanidin reductase. The conserved domains and phylogenetic relationships of these genes were characterized. The expression levels of these genes in different tissues and different ages of xylem were investigated. Additionally, the anthocyanin accumulation in xylem of different ages of T. chinensis was measured. The results showed the anthocyanin accumulation was correlated with the expression levels of dihydroflavonol 4-reductase, anthocyanidin synthase, flavonoid 3’-hydroxylase, and flavonoid 3’,5’-hydroxylase. Our results provide a basis for studying the regulation of the biosynthetic pathway for anthocyanins and wood color formation in T. chinensis.

Proanthocyanidins (PAs) play significant roles in plants and are bioactive compounds with health benefits. The polymerization mechanism has been debated for decades. Here we show that laccases (LACs) are involved in PA polymerization and miR397a is a negative regulator of PA biosynthesis in Salvia miltiorrhiza and Populus trichocarpa. Elevation of miR397a level causes significant downregulation of LACs, severe reduction of polymerized PAs, and significant increase of flavan-3-ol monomers in transgenic S. miltiorrhiza and P. trichocarpa plants. Enzyme activity analysis shows that miR397a-regulated SmLAC1 catalyzes the polymerization of flavan-3-ols and the conversion of B-type PAs to A-type. Both catechin and epicatechin can serve as the starter unit and the extension unit during PA polymerization. Overexpression of SmLAC1 results in significant increase of PA accumulation, accompanied by the decrease of catechin and epicatechin contents. Consistently, CRISPR/Cas9-mediated SmLAC1 knockout shows the opposite results. Based on these results, a scheme for LAC-catalyzed PA polymerization is proposed. The work provides insights into PA polymerization mechanism.