MOESM2 of Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

Additional file 2. Principal component analysis

MOESM1 of Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

Additional file 1. Analysis of the lignin pathway with inclusion of caffeyl aldehyde

MOESM8 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

Additional file 8: Table S7. Expression of switchgrass genes involved in hormone signaling

Additional file 1: of Transcriptome analysis of secondary cell wall development in Medicago truncatula

Supplemental Figure 1. Expression pattern analysis of cluster 10 transcription factor genes. Supplemental Figure 2. The PCC distributions in the real and random datasets. Supplemental Table 1. Distribution of differentially expressed genes in the 10 clusters. Supplemental Table 2. Probe sets and corresponding names of lignin biosynthetic genes. Supplemental Table 3. Transcription factor genes upregulated during stem maturation

MOESM11 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

Additional file 11: Table S8. The Student’s t-tests on the monosaccharide composition and sequential extraction between pairwise samples

MOESM1 of Switchgrass (Panicum virgatum L.) promoters for green tissue-specific expression of the MYB4 transcription factor for reduced-recalcitrance transgenic switchgrass

Additional file 1: Table S1. Sugars (g/g CWR) released by enzymatic hydrolysis from the transgenic switchgrass lines expressing PvMYB4 under the control of each of the three green tissue-specific promoters. Figure S1. Comparison of the deduced amino acid sequences of the rice Lhcb genes and their homologs in switchgrass. Figure S2. Comparison of the deduced amino acid sequences of the rice PEPC gene and its homologs in switchgrass. Figure S3. Comparison of the deduced amino acid sequences of the rice PsbR genes and their homologs in switchgrass. Figure S4. The gene structures of the three rice Lhcb genes (i.e., OsLhcb1-1, OsLhcb1-2, and OsLhcb2-1, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os09g17740 [54, 55, 57], Os1g41710 [54], and Os03g39610 [55], respectively) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S5. The gene structures of the five plant-type rice PEPC genes (i.e., Osppc1, 2a, 2b, 3, and 4, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os02g0244700, Os08g0366000, Os09g0315700, Os01g0758300, and Os01g0208700, respectively [56]) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S6. The gene structures of the three rice PsbR genes (i.e., OsPsbR1, 2 and 3, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os07g05360, Os07g05365, and Os08g10020, respectively [53]) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S7. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of OsLhcb1-1, OsLhcb1-2, and OsLhcb2-1, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os09g17740 [54, 55, 57], Os1g41710 [54], and Os03g39610 [55], respectively, in different tissues of non-transformed switchgrass. Figure S8. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of Osppc1, 2a, 2b, 3, and 4, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os02g0244700, Os08g0366000, Os09g0315700, Os01g0758300, and Os01g0208700, respectively [56], in different tissues of non-transformed switchgrass. Figure S9. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of OsPsbR1, 2, and 3, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os07g05360, Os07g05365, and Os08g10020, respectively [53], in different tissues of non-transformed switchgrass. Figure S10. The 764-bp-long promoter sequence of PvLhcb (i.e., Pavirv00047797m) used in the present study. Figure S11. The 1878-bp-long promoter sequence of PvPEPC (i.e., Pavirv00033161m) used in the present study. Figure S12. The 2009-bp-long promoter sequence of PvPsbR (i.e., Pavirv00009702m) used in the present study. Figure S13. Quantitative fluorometric GUS analysis of leaf blade, leaf sheath, stem, and panicles of T0 stable transgenic rice containing each serial deletion of the PvLhcb promoter at the heading stage. Figure S14. Quantitative fluorometric GUS analysis of leaf blade, leaf sheath, stem, and panicles of T0 stable transgenic rice containing each serial deletion of the PvPEPC promoter at the heading stage

BVRI photometric observations and light-curve analysis of GEO objects

BVRI photometric observations of Geosynchronous Earth Orbit (GEO) objects were conducted with the 1.5 m Cassini Telescope located in Loiano, Italy. The observatory is operated by the INAF (National Institute for Astrophysics) Astronomical Observatory of Bologna, Italy. The Ritchey–Chre´tien optical system is equipped with the BFOSC (Bologna Faint Object Spectrograph and Camera), a multipurpose instrument for imaging and spectroscopy, with an EEV CCD (13401300 pixel). This paper deals with the results of the photometric observations of several targets from the SSN (Space Surveillance Network) catalog that were acquired in May and December 2013

MOESM1 of Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass

Additional file 1. Supporting figures and tables of understanding the reduced cell wall recalcitrance of field-grown COMT Down-regulated switchgrass. Figure S1. Scheme of proposed lignin biosynthesis involving COMT. Figure S2. Relationship of cellulose DP to glucose release efficiency of unpretreated switchgrass. Figure S3. Relationship of hemicellulose molecular weights to xylose release efficiency of unpretreated switchgrass. Figure S4. Relationship of Cellulose crystallinity (CrI) to glucose release unpretreated switchgrass. Table S1. Original data used for Fig. 1: Chemical composition (per g cell wall residue) of field-grown switchgrass in years 2 and 3. The values reported are the average of 5 biological replicates from each control group, and 10 biological replicates from each transgenic group. Student t test was used as a statistical analysis for the difference between the transgenic and control groups. Table S2. Data used for Fig. 2a and b: Sugar release (mg per g cell wall residues) from hydrothermally pretreated (a) and unpretreated (b) switchgrass in years 2 and 3 after 72 h enzymatic hydrolysis (the value reported is the average of 5 biological replicates from each control group, and 10 biological replicates from each transgenic group). Student t test was used as a statistical analysis for the difference between the transgenic and control groups. Table S3. Original data used for Fig. 2c: the relationship of total sugar (glucose and xylose) release for pretreated switchgrass from enzymatic hydrolysis to lignin content (wt% of cell wall residues). Table S4. Original data used for Fig. 2d: the relationship of total sugar (glucose and xylose) release for unpretreated switchgrass from enzymatic hydrolysis to lignin content (wt% of cell wall residues). Table S5. Original data used for Figs. 3 and 4: distribution of DO adsorption and relationship of DO its relationship to sugar release (Fig. 3). Hemicellulose molecular weight distribution and Cellulose crystallinity index (CrI) (Fig. 4). Student’s t test was used as a statistical analysis for the difference between the transgenic and control groups. Table S6. Student’s t test results of traits difference in field-grown switchgrass between year 2 and 3

MOESM4 of Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance

Additional file 4. Diagram illustrating position of three RNAi construct sequences used to silence HCTs in switchgrass. Sequences amplified and expressed in switchgrass to silence HCT1 (HCT1RNAi, purple box), HCT2 (HCT2RNAi, red box), and HCT 1 and 2 together (HCT1/2RNAi, blue box) are shown within the aligned PvHCT sequences. Areas with identity between the sequences are highlighted