Conyza_canadensis_microsat

Conyza_canadensis_microsa

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

concat_alllegume.fsa

Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file

trees - bipartitions

The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files

DNA alignments

cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files

CDS translations

Corresponding CDS sequences for the peptide translations. These are multifasta files

alignments for other WGD tests

Alignments of orthogroups used to look at putative WGD events in data set. These are multifasta files

peptide translations

Peptide translations based on a blastx of the filtered Trinity assemblies to the 22 genome dataset (Amborella Genome Consortium, 2013) and conceptually translated using Genewise. These are multifasta files

RAxML_bipartitions.concat_alllegume.fsa.raxml.out

RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file

Legume pairs - ksplots

Putative paralog pairs estimated from Ks plots for multiple species from study. These were used to test for other WGD events (other than PWGD). This is a tab delimited file with the first and second columns being Ks plot identified putative paralogs and the third column being a designation for the putative event