产油皮状丝孢酵母突变株的转录组分析

对产油皮状丝孢酵母进行常压室温等离子体(ARTP)诱变,筛选得到一株高产菌株A1。为了进一步研究高产菌株A1的基因表达和代谢通路的变化,利用转录组测序手段,对原始菌株WT和高产菌株A1进行发酵培养至油脂积累最大值时,然后进行转录组测序分析。结果表明:A1与WT相比,有1185个显著基因差异表达,其中767个基因表达上调,418个基因表达下调;利用差异基因GO富集分析发现,与细胞过程、代谢过程、催化活性、细胞部分等相关的基因表现出富集;在KEEG代谢通路中,差异基因主要涉及酵母细胞周期、基因复制、戊糖和葡萄糖醛酸的相互转化、糖酵解/糖异生等过程。研究发现3个与脂肪酸积累相关的酶过表达,分别为柠檬酸合成酶、甘油磷酸二酯磷酸二酯酶、3-磷酸甘油醛脱氢酶。这些结果可为后期的油脂酵母基因改造和代谢通路调控提供理论依据。

Synthesis of Amphiphilic Starch Derivatives Using One-pot Synthesis Procedure

Amphiphilic starch derivatives with high content of functional groups were prepared from potato starch using a one-pot synthesis method with a single reaction medium for the entire procedure. Potato starch was benzylated, followed by the introduction of hydroxypropyltrimethylammonium(HPMA) moieties without the purification of intermediates. The synthesis was performed under heterogeneous conditions, leading to the formation of benzyl 2-hydroxypropyltri methylammonium starch chloride(BnHPMAS) with a total degree of substitution(DS) of up to 1.4. This process improved the efficiency of the preparation of amphiphilic starch derivatives and reduced the time and resources consumed by avoiding a separation process and purification of the intermediate compounds.The DS of BnHPMAS was in the range of 0.36 to 1.4, which could be tuned by varying the molar ratio of the reagents to repeating unit or by changing the reaction temperature, time, and medium. The structure of the amphiphilic starches was characterized using elemental analysis, size exclusion chromatography,fourier transform infrared spectroscopy(FT-IR), and nuclear magnetic resonance(NMR) spectroscopy. Moreover, the surface tension and turbidity of the solutions of the products were measured for their potential application in the removal of dissolved and colloidal substances in paper cycling water.

Cell Wall Characteristics of a Maize Mutant Selected for Decreased Ferulates

The cross-linked nature of plant cell walls provides structural integrity for continued growth and development, but limits degradation and utilization by ruminants. In grasses a major cross-linking component is ferulic acid that is incorporated into cell walls as an ester linked residue on arabinoxylans. Ferulates can become coupled to each other and to lignin forming a highly cross-linked matrix of carbohydrates and lignin. Seedling ferulate ester mutants (sfe) were produced in maize using the transposon system and evaluated in feeding trials. The work described here was undertaken to characterize changes in the ferulate cross-linked nature as well as other components of the corn cell wall matrix in leaf, sheath and stem tissues. Total ferulates decreased modestly due to the mutation and were more apparent in leaf tissue (16% - 18%) compared to sheath (+5 to?-6% change) and stem (8% - 9% decrease). The most significant changes were in the ether linked ferulates to lignin, both monomer and dehydrodiferulates (14% to 38% decrease). Other characteristics of the cell wall (lignin, neutral sugar composition) also showed modest changes. The change in total ferulates was modest, but led to improved animal performance. These findings suggest that relatively small changes can have a significant impact upon how well plant materials can be broken down and utilized by ruminants such as dairy cows.

PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

The biosynthesis of cellulose,lignin,and hemicelluloses in plant secondary cell walls(SCWs)is regulated by a hierarchical transcriptional regulatory network.This network features orthologous transcription factors shared between poplar and Arabidopsis,highlighting a foundational similarity in their genetic regulation.However,knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains limited.In this study,we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog,AtMYB103.Transgenic poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development,with fiber cells and vessels displaying thicker walls,and an increase in the levels of cellulose,lignin,and hemicelluloses in the wood.In contrast,plants with dominant repression of PagMYB128 demonstrated the opposite phenotypes.RNA sequencing and reverse transcription–quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression,and chromatin immunoprecipitation along with yeast one-hybrid,and effector–reporter assays showed this regulation was direct.Further analysis revealed that PagSND1(SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1)directly regulates PagMYB128 but not cell wall metabolic genes,highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development,thereby creating a feedforward loop in SCW biosynthesis.

Co-production of hydrochar and bioactive compounds from Ulva lactuca via a hydrothermal process

This study investigates the simultaneous production of hydrochar and bioactive compounds from Ulva lactuca via a hydrothermal process.The experiment was carried out using a batch reaction vessel at different reaction temperatures of 180-220◦C and various holding times of 30-90 min.As expected,both temperature and time vigorously influenced hydrochar and bioactive compound production.The maximum hydrochar yield was at 32.4 wt%.The higher heating value(HHV)of hydrochar was observed in the range of 17.68-21.07 MJ kg^(-1),near the energy content of low-rank coals.The hydrochars exhibited contact angles higher than 90°(i.e.,94-108°)for a longer time,confirming their hydrophobic surfaces.The scanning electron microscope analysis(SEM)showed that the hydrothermal process enables cracks in the spherical shape of raw U.lactuca into small and porous particles.Besides producing hydrochar,the hydrothermal process of U.lactuca also gives promising antioxidants and phenolics as bioactive compounds.The highest total phenolic content and antioxidant activity could be achieved in hydrolysate at 200℃and 30 min with the value of 1.20±0.12 mg/g and 71.6±1.3%,respectively.

Long-term variability of root production in bioenergy crops from ingrowth core measurements

Aims Long-term determination of root biomass production upon land-use conversion to biofuel crops is rare.To assess land-use legacy influences on belowground biomass accumulation,we converted 22-year-old Conservation Reserve Program(CRP)grasslands and 50+-year-old agricultural(AGR)lands to corn(C),switchgrass(Sw)and restored prairie(Pr)biofuel crops.We maintained one CRP grassland as a reference(Ref).We hypothesized that land-use history and crop type have significant effects on root density,with perennial crops on CRP grasslands having a higher root biomass productivity,while corn grown on former agricultural lands produce the lowest root biomass.Methods The ingrowth core method was used to determine in situ ingrowth root biomass,alongside measurements of aboveground net primary productivity(ANPP).Ancillary measurements,including air temperature,growing season length and precipitation were used to examine their influences on root biomass production.Important Findings Root biomass productivity was the highest in unconverted CRP grassland(1716 g m?2 yr?1)and lowest in corn fields(526 g m?2 yr?1).All perennial sites converted from CRP and AGR lands had lower root biomass and ANPP in the first year of planting but peaked in 2011 for switchgrass and a year later for restored prairies.Ecosystem stability was higher in restored prairies(AGR-Pr:4.3±0.11;CRP-Pr:4.1±0.10),with all monocultures exhibiting a lower stability.Root biomass production was positively related to ANPP(R2=0.40).Overall,attention should be given to root biomass accumulation in large-scale biofuel production as it is a major source of carbon sequestration.

Net primary production in three bioenergy crop systems following land conversion

Aims Identifying the amount of production and the partitioning to above-and belowground biomass is generally the first step toward select-ing bioenergy systems.There are very few existing studies on the dynamics of production following land conversion.The objectives of this study were to(i)determine the differences in aboveground net primary production(ANPP),belowground net primary produc-tion(BNPP),shoot-to-root ratio(S:R)and leaf area index in three bioenergy crop systems and(ii)evaluate the production of these three systems in two different land use conversions.Methods This investigation included biometric analysis of NPP on three agri-cultural sites converted from conservation reserve program(CRP)management to bioenergy crop production(corn,switchgrass and prairie mix)and three sites converted from traditional agriculture production to bioenergy crop production.Important findings The site converted from conventional agriculture produced smaller ANPP in corn(19.03±1.90 standard error[SE]Mg ha^(−1) year^(−1))than the site converted from CRP to corn(24.54±1.43 SE Mg ha^(−1) year^(−1)).The two land conversions were similar in terms of ANPP for switchgrass(4.88±0.43 SE for CRP and 2.04±0.23 SE Mg ha^(−1) year^(−1) for agriculture)and ANPP for prairie mix(4.70±0.50 SE for CRP and 3.38±0.33 SE Mg ha^(−1) year^(−1) for agriculture).The BNPP at the end of the growing season in all the bioenergy crop systems was not significantly different(P=0.75,N=8).

Denitrification and the challenge of scaling microsite knowledge to the globe

Our knowledge of microbial processes—who is responsible for what,the rates at which they occur,and the substrates consumed and products produced—is imperfect for many if not most taxa,but even less is known about how microsite processes scale to the ecosystem and thence the globe.In both natural and managed environments,scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes.But rarely is scaling straightforward:More often than not,process rates in situ are distributed in a highly skewed fashion,under the influence of multiple interacting controls,and thus often difficult to sample,quantify,and predict.To date,quantitative models of many important processes fail to capture daily,seasonal,and annual fluxes with the precision needed to effect meaningful management outcomes.Nitrogen cycle processes are a case in point,and denitrification is a prime example.Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions.Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced.Incorporating trait-based models into such efforts promises to improve predictions and understanding still further,but much more development is needed.

QT-GWAS:A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits

Although the plant kingdom provides an enormous diversity of metabolites with potentially beneficial applications for humankind,a large fraction of these metabolites and their biosynthetic pathways remain unknown.Resolving metabolite structures and their biosynthetic pathways is key to gaining biological understanding andto allow metabolic engineering.In orderto retrieve novel biosynthetic genes involved in specialized metabolism,we developed a novel untargeted method designated as qualitative trait GWAs(QT-GWAS)that subjects qualitative metabolic traits to a genome-wide association study,while the conventional metabolite GWAS(mGWAS)mainly considers the quantitative variation of metabolites.As a proof of the validity of QT-GWAS,23 and 15of the retrieved associations identified in Arabidopsis thaliana by QTGWAS and mGWAS,respectively,were supported by previous research.Furthermore,seven genemetabolite associations retrieved by QT-GWAS were confirmed in this study through reverse genetics combined with metabolomics and/or in vitro enzyme assays.As such,we established that CYTOCHROME P450706A5(CYP706A5)is involved in the biosynthesis of chroman derivatives,UDP-GLYCOSYLTRANSFERASE 76C3(UGT76C3)is able tohexosylate guanine in vitro and in planta,and SULFOTRANSFERASE 202B1(SULT202B1)catalyzes the sulfation of neolignans in vitro.Collectively,our study demonstrates that the untargeted QT-GWAS method can retrieve valid gene-metabolite associations at the level of enzyme-encoding genes,even new associations that cannot be found by the conventional mGwAs,providing a new approach for dissecting qualitative metabolic traits.

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO_(2)and H_(2)

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO_(2) emissions make CO_(2) an attractive feedstock for manufacturing chemicals.Moreover,H_(2) is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water(scH_(2)O) gasification enable sustainable production of molecular hydrogen(H_(2)).We review the recent advances in engineering Ralsto-nia eutropha,the representative species of“Knallgas”bacteria,for utilizing CO_(2) and H_(2) to autotrophically produce 2,3-butanediol(2,3-BDO).This assessment is focused on state-of-the-art approaches for splitting H_(2) to supply en-ergy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO_(2) fixation.Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO_(2) and H_(2)-utilizing microorganisms,exemplified by Zymomonas mobilis.

Meta-QC-Chain:Comprehensive and Fast Quality Control Method for Metagenomic Data

Next-generation sequencing （NGS） technology has revolutionized and significantly impacted metagenomic research.However,the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating reads,which will significantly compromise downstream analysis.Many quality control （QC） tools have been proposed,however,few of them have been verified to be suitable or efficient for metagenomic data,which are composed of multiple genomes and are more complex than other kinds of NGS data.Here we present a metagenomic data QC method named Meta-QC-Chain.Meta-QC-Chain combines multiple QC functions： technical tests describe input data status and identify potential errors,quality trimming filters poor sequencing-quality bases and reads,and contamination screening identifies higher eukaryotic species,which are considered as contamination for metagenomic data.Most computing processes are optimized based on parallel programming.Testing on an 8-GB real dataset showed that Meta-QC-Chain trimmed low sequencing-quality reads and contaminating reads,and the whole quality control procedure was completed within 20 min.Therefore,Meta-QC-Chain provides a comprehensive,useful and high-performance QC tool for metagenomic data.Meta-QC-Chain is publicly available for free at： http：//computationalbioenergy.org/meta-qc-chain.html.

Arthropods and biofuel production systems in North America

Biomass harvest may eventually be conducted on over 100 000 000 ha of US crop and forest lands to meet federally-mandated targets for renewable biofuels. Such largescale land use changes could profoundly impact working landscapes and the arthropod communities that inhabit them. We review the literature on dedicated biofuel crops and biomass harvest from forests to look for commonalities in arthropod community responses. With expanded biofuel production, existing arthropod pests of biofuel crops will likely become more important and new pests will emerge. Beneficial arthropods will also be influenced by biofuel crop habitats, potentially altering the distribution of pollination and pest control services to the surrounding landscape. Production of biofuel crops including initial crop selection, genetic improvement, agronomic practices, and harvest regimes will also influence arthropod communities. In turn, arthropods will impact the productivity and species composition of biomass production systems. Some of these processes have the potential to cause landscape-level changes in arthropod community dynamics and insect- vectored plant diseases. Finally, changes in arthropod populations and their spatiotemporal distribution in the landscape will have impacts on consumers of insects at higher trophic levels, potentially influencing their population and community dynamics and producing feedbacks to arthropod communities. Given that dedicated biofuel crops and intensified biomass harvest from forests are still relatively uncommon in North America, as they increase, we anticipate ＇predictably unpredictable＇ shifts in arthropod communities and the ecosystem services and functions they support. We suggest that research on arthropod dynamics within biofuel crops, their spillover into adjacent habitats, and implications for the sustainability of working landscapes are critical topics for both basic and applied investigations.

Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthesis of Pectin and Xylan in Cell Walls and Seed Testa

Galacturonosyltransferase 1 （GAUT1） is an α1,4-D-galacturonosyltransferase that transfers galacturonic acid from uridine 5＇-diphosphogalacturonic acid onto the pectic polysaccharide homogalacturonan （Sterling et al., 2006）. The 25-member Arabidopsis thaliana GAUT1-related gene family encodes 15 GAUT and 10 GAUT-like （GATL） proteins with, respectively, 56-84 and 42-53% amino acid sequence similarity to GAUT1. Previous phylogenetic analyses of AtGAUTs indicated three clades： A through C. A comparative phylogenetic analysis of the Arabidopsis, poplar and rice GAUT families has sub-classified the GAUTs into seven clades： clade A-1 （GAUTs 1 to 3）; A-2 （GAUT4）; A-3 （GAUTs 5 and 6）; A-4 （GAUT7）; B-1 （GAUTs 8 and 9）; B-2 （GAUTs 10 and 11）; and clade C （GAUTs 12 to 15）. The Arabidopsis GAUTs have a distribution comparable to the poplar orthologs, with the exception of GAUT2, which is absent in poplar. Rice, however, has no orthologs of GAUTs 2 and 12 and has multiple apparent orthologs of GAUTs 1, 4, and 7 compared with eitherArabidopsis or poplar. The cell wall glycosyl residue compositions of 26 homozygous T-DNA insertion mutants for 13 of 15 Arabidopsis GAUTgenes reveal significantly and reproducibly different cell walls in specific tissues of gaut mutants 6, 8, 9, 10, 11, 12, 13, and 14 from that of wild-type Arabidopsis walls. Pectin and xylan polysaccharides are affected by the loss of GAUT function, as demonstrated by the altered galacturonic acid, xylose, rhamnose, galactose, and arabinose composition of distinct gaut mutant walls. The wall glycosyl residue compositional phenotypes observed among the gaut mutants suggest that at least six different biosynthetic linkages in pectins and/or xylans are affected by the lesions in these GAUTgenes. Evidence is also presented to support a role for GAUT11 in seed mucilage expansion and in seed wall and mucilage composition.

Two Poplar Glycosyltransferase Genes, PdGATL 1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL 1 in Arabidopsis

Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of wood, is poorly understood. Here, we characterize two Populus genes, PdGATL 1.1 and PdGATL 1.2, the closest orthologs to the Arabidopsis PARVUS/GATL1 gene, with respect to their gene expression in poplar, their sub-cellular localization, and their ability to complement the parvus mutation in Arabidopsis. Overexpression of the two poplar genes in the parvus mutant rescued most of the defects caused by the parvus mutation, including morphological changes, collapsed xylem, and altered cell wall monosaccharide composition. Quantitative RT-PCR showed that PdGATL1.1 is expressed most strongly in developing xylem of poplar. In contrast, PdGATL1.2 is expressed much more uniformly in leaf, shoot tip, cortex, phloem, and xylem, and the transcript level of PdGATL1.2 is much lower than that of PdGATL 1.1 in all tissues examined. Sub-cellular localization experiments showed that these two proteins are localized to both ER and Golgi in comparison with marker proteins resident to these sub-cellular compartments. Our data indicate that PdGATLI.1 and PdGATL1.2 are functional orthologs of PARVUS/ GATL1 and can play a role in xylan synthesis, but may also have role（s） in the synthesis of other wall polymers.

Large-Scale Analyses of Glycosylation in Cellulases

Cellulases are important glycosyl hydrolases （GHs） that hydrolyze cellulose polymers into smaller oligosaccharides by breaking the cellulose β （1→4） bonds, and they are widely used to produce cellulosic ethanol from the plant biomass. N-linked and O-linked glycosylations were proposed to impact the catalytic efficiency, cellulose binding affinity and the stability of cellulases based on observations of individual cellulases. As far as we know, there has not been any systematic analysis of the distributions of N-linked and O-linked glycosylated residues in cellulases, mainly due to the limited annotations of the relevant functional domains and the glycosylated residues. We have computationally annotated the functional domains and glycosylated residues in cellulases, and conducted a systematic analysis of the distributions of the N-linked and O-linked glycosylated residues in these enzymes. Many N-linked glycosylated residues were known to be in the GH domains of cellulases, but they are there probably just by chance, since the GH domain usually occupies more than half of the sequence length of a cellulase. Our analysis indicates that the O-linked glycosylated residues are significantly enriched in the linker re- gions between the carbohydrate binding module （CBM） domains and GH domains of cellulases. Possible mechanisms are discussed.

Virus-Induced Gene Silencing Offers a Functional Genomics Platform for Studying Plant Cell Wall Formation

Virus-induced gene silencing （VIGS） is a powerful genetic tool for rapid assessment of plant gene functions in the post-genomic era. Here, we successfully implemented a Tobacco Rattle Virus （TRV）-based VlGS system to study functions of genes involved in either primary or secondary cell wall formation in Nicotiana benthamiana plants. A 3-week post- VIGS time frame is sufficient to observe phenotypic alterations in the anatomical structure of stems and chemical composition of the primary and secondary cell walls. We used cell wall glycan-directed monoclonal antibodies to demonstrate that alteration of cell wall polymer synthesis during the secondary growth phase of VIGS plants has profound effects on the extractability of components from woody stem cell walls. Therefore, TRV-based VlGS together with cell wall component profiling methods provide a high-throughput gene discovery platform for studying plant cell wall formation from a bioenergy perspective.

RNA-Seq Analysis of Developing Nasturtium Seeds （Tropaeolum majus）： Identification and Characterization of an Additional Galactosyltransferase Involved in Xyloglucan Biosynthesis

A deep-sequencing approach was pursued utilizing 454 and Illumina sequencing methods to discover new genes involved in xyloglucan biosynthesis, cDNA sequences were generated from developing nasturtium （Tropaeolum majus） seeds, which produce large amounts of non-fucosylated xyloglucan as a seed storage polymer. In addition to known xyloglucan biosynthetic genes, a previously uncharacterized putative xyloglucan galactosyltransferase was iden- tified. Analysis of an Arabidopsis thaliana mutant line defective in the corresponding ortholog （AT5G62220） revealed that this gene shows no redundancy with the previously characterized xyloglucan galactosyltransferase, MUR3, but is required for galactosyl-substitution of xyloglucan at a different position. The gene was termed XLT2 for Xyloglucan L-side chain galactosylTransferase position 2. It represents an enzyme in the same subclade of glycosyltransferase family 47 as MUR3. A double mutant defective in both MUR3 （mur3.1） and XLT2 led to an Arabidopsis plant with xyloglucan that consists essentially of only xylosylated glucosyl units, with no further substitutions.

Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency

The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of the organization of a genome. Here we address an important and chal- lenging question regarding the global arrangement of operons in a bacterial genome： why operons in a bacterial genome are arranged in the way they are. We have previously studied this question and found that operons of more frequently activated pathways tend to be more clustered together in a genome. Specifically, we have developed a simple sequential distance-based pseudo energy func- tion and found that the arrangement of operons in a bacterial genome tend to minimize the clus- teredness function （C value） in comparison with artificially-generated alternatives, for a variety of bacterial genomes. Here we extend our previous work, and report a number of new observations： （a） operons of the same pathways tend to group into a few clusters rather than one; and （b） the global arrangement of these operon clusters tend to minimize a new ＂energy＂ function （C＋ value） that reflects the efficiency of the transcriptional activation of the encoded pathways. These obser- vations provide insights into further study of the genomic organization of genes in bacteria.

Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons.One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency property.More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.

MYB46-Mediated Transcriptional Regulation of Secondary Wall Biosynthesis

Formation of secondary wall requires coordinated transcrip- tional regulation of the genes involved in the biosynthesis of major secondary wall components （e.g. cellulose, hemicellu- lose, and lignin）. Even though many aspects of plant biology have been extensively elucidated using various model spe- cies, our current understanding of secondary wall formation is limited.