Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.

Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An Arabidopsis double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in Populus trichocarpa. To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed PtrMIR397a in transgenic P. trichocarpa. In each of all nine transgenic lines tested, 17 PtrLACs were down-regulated as analyzed by RNAseq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of Ptr-MIR397a in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis. Full transcriptome-based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content.L ignin, an abundant biological polymer affecting the ecology of the terrestrial biosphere, is vital for the integrity of plant cell walls, the strength of stems, and resistance against pests and pathogens (1). Lignin is also a major barrier in the pulping and biomass-to-ethanol processes (2-4). For extracting cellulose (pulping) or for enzymatic degradation of cellulose for bioethanol, harsh chemical or physical treatments are used to reduce interactions with lignin or other cell wall components (2-4). Reducing lignin content or altering lignin structure to reduce its recalcitrance are major goals for more efficient processing.Lignin is polymerized primarily from three monolignol precursors, p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol (1, 5). Over five decades, efforts have been made to understand the biosynthesis of the primary monolignols and to modify the quantity or composition of lignin. The polymerization of monolignols into a lignin polymer has long been thought to occur through oxidative polymerization catalyzed by either laccases or peroxidases (6). The mechanisms and specificity of the roles of the oxidative enzymes in lignin polymerization have been controversial (7).Laccases (EC. 1.10.3.2) are multicopper oxidoreductases. Plant laccase was the first enzyme sh...

Cellulolytic enzyme lignin (CEL) and milled wood lignin (MWL) were prepared by three different ball-milling methods. The structure of CEL at various yields was elucidated and compared with MWL using wet chemical analysis, FTIR and solution-state NMR techniques. Results show that ball milling of wood degrades β-O-4 structures in lignin. However, even after extensive ball milling, less than 25% of the β-O-4 structures were degraded. The extent of degradation was less for softwood than for hardwood lignin. Extractable lignin yield, either MWL or CEL, was the best way to assess the extent and effect of ball milling. CEL is preferred over MWL, as it can be isolated in higher yield with less degradation. CEL was isolated at yields ranging from 20% to 86%. Over this range the CEL had similar structures, suggesting that lignin in the secondary wall is uniform in structure. The residual enzyme lignin (REL) was structurally different from CEL and may originate mainly from the middle lamella. In this paper we propose a new procedure for the isolation of lignin for use in structural studies, whereby wood is sufficiently milled and successively extracted to produce three lignin fractions representing the total lignin in wood.

A rapid transmittance near-infrared (NIR) spectroscopic method has been developed to characterize the lignin content of solid wood. Using simple, multiple regression, and partial least-squares statistical analysis the lignin contents of wood wafers, taken from increment cores, and synthetic wood, prepared by blending milled wood lignin and holocellulose, were compared and quantified. Strong correlations were obtained between the predicted NIR results and those obtained from traditional chemical methods. In addition to the experimental protocol and method development, NIR results from wood samples with different particle sizes and various lignin contents are discussed.

To better understand the within-tree variations between juvenile wood, mature wood, and compression wood, wood from a 35-year-old mature bent loblolly pine was separated into seven groups by different positions in the tree. Morphological and chemical structure analyses, including fiber quality, X-ray diffraction, sugar and lignin content analysis, as well as nitrobenzene oxidation, ozonation, and advanced NMR spectroscopy, were performed. Fiber properties were significantly different for tree-top juvenile normal wood and tree-bottom juvenile normal wood, juvenile normal and mature normal wood, juvenile compression and mature compression wood. However, differences in the chemical structure and composition were less significant within the specific tissues indicated above.

A rapid transmittance near-infrared (NIR) spectroscopy method was developed to predict the variation in chemical composition of solid wood. The effect of sample preparation, sample quantity (single versus stacked multiple wood wafers), and NIR acquisition time on the quantification of alpha-cellulose and lignin content was investigated. Strong correlations were obtained between laboratory wet chemistry values and the NIR-predicted values. In addition to the experimental protocol and method development, improvements in calibration error associated with utilizing stacked multiple wood wafers as opposed to single wood wafers are also discussed.

In conifers, juvenile wood (JW) is always associated with compression wood (CW). Due to their similar properties, there is a common belief that JW is the same as CW. To resolve whether JW is identical to CW, 24 rooted cuttings of one loblolly pine clone were planted in growth chambers under normal, artificial bending, and windy environments. The results show that the morphology of JW is significantly different from CW. Furthermore, chemical analyses revealed that JW and CW are significantly different in chemical composition. Our results indicate that JW is different from CW, and the wood formed under a controlled windy environment is a mild type of compression wood.

Genetic engineering of trees has generated a large amount of interest in the development of highly improved transgenic trees. To efficiently monitor and control the properties of the transgenic products, a rapid, mini-scale analytical method is required. Transmittance near-infrared (NIR) spectroscopy was chosen as a fast analysis tool for characterizing the chemical properties of the transgenic products. Pellets were prepared from 75 mg of wood meal and directly scanned using transmittance NIR spectroscopy. Very strong correlations were obtained between the NIR data and conventional wet-chemistry results for the lignin content, S/G ratio, cellulose and xylose content. The results indicate that transmittance NIR is a powerful tool for determining and screening the chemical properties of transgenic trees.