Data from: Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiosperms

Lignin and flavonoids play a vital role in the adaption of plants to a terrestrial environment. 4-Coumarate: coenzyme A ligase (4CL) is a key enzyme of general phenylpropanoid metabolism which provides the precursors for both lignin and flavonoids biosynthesis. However, very little is known about how such essential enzymatic functions evolve and diversify. Here, we analyze 4CL sequence variation patterns in a phylogenetic framework to further identify the evolutionary forces that lead to functional divergence. The results reveal that lignin-biosynthetic 4CLs are under positive selection. The majority of the positively selected sites are located in the substrate-binding pocket and the catalytic center, indicating that nonsynonymous substitutions might contribute to the functional evolution of 4CLs for lignin biosynthesis. The evolution of 4CLs involved in flavonoid biosynthesis is constrained by purifying selection and maintains the ancestral role of the protein in response to biotic and abiotic factors. Overall, our results demonstrate that protein sequence evolution via positive selection is an important evolutionary force driving adaptive diversification in 4CL proteins in angiosperms. This diversification is associated with adaption to a terrestrial environment

Additional file 1 of Overexpression of PtoMYB115 improves lignocellulose recalcitrance to enhance biomass digestibility and bioethanol yield by specifically regulating lignin biosynthesis in transgenic poplar

Additional file 1: Table S1. Gene primers used in this study. Figure S1. Measurement of plant growth and gene expression in transgenic poplar plants. (a) Images of 3-month-old transgenic poplar lines and wild type (WT); Scale bar as 10 cm. (b) Expression of cell differentiation genes in PtoMYB115 transgenic plants and WT. Primers are listed in Table S1. The poplar ubiquitin gene was used as an internal control. All data are given as means ± SD from three biological repeats. Statistical analyses were performed using Student’s t test as **P < 0.01 (n = 3). Figure S2. Observations of plant cell wall formation in the PtoMYB115 transgenic lines and WT. (a) Cell wall thickness of SEM observation; (b) Cellulose and hemicellulose contents (% biomass). All data as means ± SD. Student’s t-test was performed between the transgenic line and WT as **P < 0.01 (n = 3). Figure S3. Comparison of lignocellulose features between the transgenic lines and WT. (a) Crystalline index (CrI) of crude cellulose. (b) Correlation analysis between lignocellulose features and hexose yields (% biomass) released from enzymatic hydrolyses after H2SO4 or CaO pretreatment. **Significant correlation at P < 0.01 (n = 15). Figure S4. Correlation analysis between DP of cellulose and hexose yields (% biomass) released from enzymatic hydrolyses after pretreatments. Figure S5. Quantitative RT-PCR analysis of proanthocyanidin biosynthetic genes in the PtoMYB115 transgenic lines and WT

Sugar-rich sweet sorghum is distinctively affected by wall polymer features for biomass digestibility and ethanol fermentation in bagasse

Sweet sorghum has been regarded as a typical species for rich soluble-sugar and high lignocellulose residues, but their effects on biomass digestibility remain unclear. In this study, we examined total 63 representative sweet sorghum accessions that displayed a varied sugar level at stalk and diverse cell wall composition at bagasse. Correlative analysis showed that both soluble-sugar and dry-bagasse could not significantly affect lignocellulose saccharification under chemical pretreatments. Comparative analyses of five typical pairs of samples indicated that DP of crystalline cellulose and arabinose substitution degree of non-KOH-extractable hemicelluloses distinctively affected lignocellulose crystallinity for high biomass digestibility. By comparison, lignin could not alter lignocellulose crystallinity, but the KOH-extractable G-monomer predominately determined lignin negative impacts on biomass digestions, and the G-levels released from pretreatments significantly inhibited yeast fermentation. The results also suggested potential genetic approaches for enhancing soluble-sugar level and lignocellulose digestibility and reducing ethanol conversion inhibition in sweet sorghum. (C) 2014 Published by Elsevier Ltd

A near infrared spectroscopic assay for stalk soluble sugars, bagasse enzymatic saccharification and wall polymers in sweet sorghum

In this study, 123 sweet sorghum (Sorghum bicolor L.) accessions and 50 mutants were examined with diverse stalk soluble sugars, bagasse enzymatic saccharification and wall polymers, indicating the potential near infrared spectroscopy (NIRS) assay for those three important parameters. Using the calibration and validation sets and modified squares method, nine calibration optimal equations were generated with high determination coefficient on the calibration (R-2) (0.81-0.99), cross-validation (R(2)cv) (0.77-0.98), and the ratio performance deviation (RPD) (2.07-7.45), which were at first time applied by single spectra for simultaneous assay of stalk soluble sugars, bagasse hydrolyzed sugars, and three major wall polymers in bioenergy sweet sorghum. (C) 2014 Elsevier Ltd. All rights reserved

A near infrared spectroscopic assay for stalk soluble sugars, bagasse enzymatic saccharification and wall polymers in sweet sorghum

In this study, 123 sweet sorghum (Sorghum bicolor L.) accessions and 50 mutants were examined with diverse stalk soluble sugars, bagasse enzymatic saccharification and wall polymers, indicating the potential near infrared spectroscopy (NIRS) assay for those three important parameters. Using the calibration and validation sets and modified squares method, nine calibration optimal equations were generated with high determination coefficient on the calibration (R-2) (0.81-0.99), cross-validation (R(2)cv) (0.77-0.98), and the ratio performance deviation (RPD) (2.07-7.45), which were at first time applied by single spectra for simultaneous assay of stalk soluble sugars, bagasse hydrolyzed sugars, and three major wall polymers in bioenergy sweet sorghum. (C) 2014 Elsevier Ltd. All rights reserved

AtCesA8-driven OsSUS3 expression leads to largely enhanced biomass saccharification and lodging resistance by distinctively altering lignocellulose features in rice

Abstract Background Biomass recalcitrance and plant lodging are two complex traits that tightly associate with plant cell wall structure and features. Although genetic modification of plant cell walls can potentially reduce recalcitrance for enhancing biomass saccharification, it remains a challenge to maintain a normal growth with enhanced biomass yield and lodging resistance in transgenic plants. Sucrose synthase (SUS) is a key enzyme to regulate carbon partitioning by providing UDP-glucose as substrate for cellulose and other polysaccharide biosynthesis. Although SUS transgenic plants have reportedly exhibited improvement on the cellulose and starch based traits, little is yet reported about SUS impacts on both biomass saccharification and lodging resistance. In this study, we selected the transgenic rice plants that expressed OsSUS3 genes when driven by the AtCesA8 promoter specific for promoting secondary cell wall cellulose synthesis in Arabidopsis. We examined biomass saccharification and lodging resistance in the transgenic plants and detected their cell wall structures and wall polymer features. Results During two-year field experiments, the selected AtCesA8::SUS3 transgenic plants maintained a normal growth with slightly increased biomass yields. The four independent transgenic lines exhibited much higher biomass enzymatic saccharification and bioethanol production under chemical pretreatments at P < 0.01 levels, compared with the controls of rice cultivar and empty vector transgenic line. Notably, all transgenic lines showed a consistently enhanced lodging resistance with the increasing extension and pushing forces. Correlation analysis suggested that the reduced cellulose crystallinity was a major factor for largely enhanced biomass saccharification and lodging resistance in transgenic rice plants. In addition, the cell wall thickenings with the increased cellulose and hemicelluloses levels should also contribute to plant lodging resistance. Hence, this study has proposed a mechanistic model that shows how OsSUS3 regulates cellulose and hemicelluloses biosyntheses resulting in reduced cellulose crystallinity and increased wall thickness, thereby leading to large improvements of both biomass saccharification and lodging resistance in transgenic rice plants. Conclusions This study has demonstrated that the AtCesA8::SUS3 transgenic rice plants exhibited largely improved biomass saccharification and lodging resistance by reducing cellulose crystallinity and increasing cell wall thickness. It also suggests a powerful genetic approach for cell wall modification in bioenergy crops

Distinct Geographical Distribution of the <i>Miscanthus</i> Accessions with Varied Biomass Enzymatic Saccharification

<div><p><i>Miscanthus</i> is a leading bioenergy candidate for biofuels, and it thus becomes essential to characterize the desire natural <i>Miscanthus</i> germplasm accessions with high biomass saccharification. In this study, total 171 natural <i>Miscanthus</i> accessions were geographically mapped using public database. According to the equation [P(H/L| East) = P(H/L∩East)/P(East)], the probability (P) parameters were calculated on relationships between geographical distributions of <i>Miscanthus</i> accessions in the East of China, and related factors with high(H) or low(L) values including biomass saccahrification under 1% NaOH and 1% H₂SO₄ pretreatments, lignocellulose features and climate conditions. Based on the maximum P value, a golden cutting line was generated from 42°25’ N, 108°22’ E to 22°58’ N, 116°28’ E on the original locations of <i>Miscanthus</i> accessions with high P(H|East) values (0.800–0.813), indicating that more than 90% <i>Miscanthus</i> accessions were originally located in the East with high biomass saccharification. Furthermore, the averaged insolation showed high P (H|East) and P(East|H) values at 0.782 and 0.754, whereas other climate factors had low P(East|H) values, suggesting that the averaged insolation is unique factor on <i>Miscanthus</i> distributions for biomass saccharification. In terms of cell wall compositions and wall polymer features, both hemicelluloses level and cellulose crystallinity (CrI) of <i>Miscanthus</i> accessions exhibited relative high P values, suggesting that they should be the major factors accounting for geographic distributions of <i>Miscanthus</i> accessions with high biomass digestibility.</p></div

Variation of Cell wall compositions in four <i>Miscanthus</i> species.

<p>Variation of Cell wall compositions in four <i>Miscanthus</i> species.</p

Geographic distribution of four <i>Miscanthus</i> species in China.

<p>(<b>a</b>) <i>Miscanthus</i> growth; (<b>b</b>) Map of <i>Miscanthus</i> locations.</p