A transcriptomic view to wounding response in young Scots pine stems

Multifunctional 5-hydroxyconiferaldehyde O-methyltransferases (CAldOMTs) in plant metabolism

Lignin, flavonoids, melatonin, and stilbenes are plant specialized metabolites with diverse physiological and biological functions, supporting plant growth and conferring stress resistance. Their biosynthesis requires O-methylations catalyzed by 5-hydroxyconiferaldehyde O-methyltransferase (CAldOMT; also called caffeic acid O-methyltransferase, COMT). CAldOMT was first known for its roles in syringyl (S) lignin biosynthesis in angiosperm cell walls and later found to be multifunctional. This enzyme also catalyzes O-methylations in flavonoid, melatonin, and stilbene biosynthetic pathways. Phylogenetic analysis indicated the convergent evolution of enzymes with OMT activities towards the monolignol biosynthetic pathway intermediates in some gymnosperm species that lack S-lignin and Selaginella moellendorffii, a lycophyte which produces S-lignin. Furthermore, neofunctionalization of CAldOMTs occurred repeatedly during evolution, generating unique O-methyltransferases (OMTs) with novel catalytic activities and/or accepting novel substrates, including lignans, 1,2,3-trihydroxybenzene, and phenylpropenes. This review summarizes multiple aspects of CAldOMTs and their related proteins in plant metabolism and discusses their evolution, molecular mechanism, and roles in biorefineries, agriculture, and synthetic biology.

Transcriptional Regulation of Female and Male Flower Bud Initiation and Development in Pecan (Carya illinoensis)

Pecan (Carya illinoensis) nuts are delicious and rich in unsaturated fatty acids, which are beneficial for human health. Their yield is closely related to several factors, such as the ratio of female and male flowers. We sampled and paraffin-sectioned female and male flower buds for one year and determined the stages of initial flower bud differentiation, floral primordium formation, and pistil and stamen primordium formation. We then performed transcriptome sequencing on these stages. Our data analysis suggested that FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 play a role in flower bud differentiation. J3 was highly expressed in the early stage of female flower buds and may play a role in regulating flower bud differentiation and flowering time. Genes such as NF-YA1 and STM were expressed during male flower bud development. NF-YA1 belongs to the NF-Y transcription factor family and may initiate downstream events leading to floral transformation. STM promoted the transformation of leaf buds to flower buds. AP2 may have been involved in the establishment of floral meristem characteristics and the determination of floral organ characteristics. Our results lay a foundation for the control and subsequent regulation of female and male flower bud differentiation and yield improvement.

Wounding rapidly alters transcription factor expression, hormonal signaling, and phenolic compound metabolism in harvested sugarbeet roots

Injuries sustained by sugarbeet (Beta vulgaris L.) roots during harvest and postharvest operations seriously reduce the yield of white sugar produced from stored roots. Although wound healing is critically important to reduce losses, knowledge of these processes is limited for this crop as well as for roots in other species. To better understand the metabolic signals and changes that occur in wounded roots, dynamic changes in gene expression were determined by RNA sequencing and the activity of products from key genes identified in this analysis were determined in the 0.25 to 24 h following injury. Nearly five thousand differentially expressed genes that contribute to a wide range of cellular and molecular functions were identified in wounded roots. Highly upregulated genes included transcription factor genes, as well as genes involved in ethylene and jasmonic acid (JA) biosynthesis and signaling and phenolic compound biosynthesis and polymerization. Enzyme activities for key genes in ethylene and phenolic compound biosynthesis and polymerization also increased due to wounding. Results indicate that wounding causes a major reallocation of metabolism in sugarbeet taproots. Although both ethylene and JA are likely involved in triggering wound responses, the greater and more sustained upregulation of ethylene biosynthesis and signaling genes relative to those of JA, suggest a preeminence of ethylene signaling in wounded sugarbeet roots. Changes in gene expression and enzymes involved in phenolic compound metabolism additionally indicate that barriers synthesized to seal off wounds, such as suberin or lignin, are initiated within the first 24 h after injury.

Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation

Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.

Adaptive strategies of Scots pine under shade: Increase in lignin synthesis and ecotypic variation in defense-related gene expression

Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growing season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defense-related genes (growth-defense trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defense-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.

Changes in the Differentiation Program of Birch Cambial Derivatives following Trunk Girdling

The mechanisms regulating the tree trunk radial growth can be studied in original experiments. One technique for studying cambium activity (the meristem involved in radial growth) under conditions of an increased photoassimilate level is trunk girdling. We girdled the trunks of 17- to 22-year-old silver birch plants (Betula pendula Roth var. pendula) during the active growth period and collected xylem and phloem samples at two height levels (1 cm and 35 cm) above girdle, 10, 20, and 30 days after girdling. We investigated the changes that occurred at the anatomical level, as well as the activities of sucrose-metabolizing enzymes and antioxidant-system enzymes and the expression of genes that encode proteins involved in sucrose and auxin transport and metabolism. A moderate increase in photoassimilates (35 cm above the girdle) resulted in a change in the ratio of phloem to xylem increments and an increase in the proportion of parenchyma in the conducting tissues. The increase of photoassimilates above the level at which they can be used in the processes of normal tissue growth and development (1 cm above the girdle) led to xylogenesis suppression and the stimulation of phloem formation, a significant increase in the parenchyma proportion in the conducting tissues, and formation of large sclereid complexes. The differentiation of parenchyma and sclereid cells coincided with biochemical and molecular markers of abnormal conducting tissue formation in Karelian birch, which are also characterized by high proportions of parenchyma and sclereid near the cambium. The results obtained are important in understanding the cambium responses to the photoassimilate distribution changes and estimating tree productivity and survival under changing environmental conditions.

Analysis of Transcriptome and Terpene Constituents of Scots Pine Genotypes Inherently Resistant or Susceptible to Heterobasidion annosum

Root and stem rot caused by Heterobasidion annosum is a severe problem in boreal Scots pine. Dissecting the features of disease resistance is generally an essential step in resistance breeding in plants and forest trees. In this study, we explored inherent resistance factors of Scots pine against H. annosum. A total of 236 families consisting of 85 full-sib (FS), 35 half-sib population mix (HSpm), and 116 half-sib (HS) families of Scots pine seedlings were inoculated with a H. annosum isolate. We sampled needle tissues before inoculation for terpene measurements and RNA sequencing. Based on the lesion area, the extremes of 12 resistant and 12 susceptible families were selected for further analyses. Necrotic lesions resulting from fungal infection were in a weak to moderate relationship with the plant height. Monoterpenes were the principal terpene compounds observed in Scots pine seedlings. Concentrations of 3-carene were significantly higher in pine genotypes inherently resistant compared with susceptible seedlings. By contrast, susceptible genotypes had significantly higher proportions of α-pinene. Gene ontology analysis of differential expressed transcripts (DETs) revealed that response to biotic factors was enriched in resistant seedlings. Functional characterization of individual DETs revealed that higher expression of transcripts involved in response to abiotic stress was common in susceptible genotypes. This observation was supported by the annotation of hub genes in a key module that was significantly correlated with the lesion trait through weighted gene co-expression network analysis (WGCNA) of 16 HS and HSpm samples. These findings contribute to our understanding of constitutive resistance factors of Scots pine against Heterobasidion root and stem rot diseases.