Research Notes : United States : Superoxide dismutase (SOD) in soybean

We are using vertical polyacrylamide gel electrophoresis (Davis, 1964) and a staining system modified after Beauchamp and Fridovich (1971) to study superoxide dismutase polymorphisms in the subgenus soja. This staining system generates superoxide radical; hence, it is specific for SOD activity. We re-solve up to 9 SOD bands in dry or germinating soybean cotyledons, and in leaves

Additional file 6: Figure S3. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Phylogenetic relationship of Medicago based on phased alleles and majority consensus sequences, genes 5 and 6. For details see Additional file 4: Figure S1. (PDF 575 kb

Additional file 1: Table S1. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Species used in this study along with accession numbers. PI and W6 numbers are from United States Department of Agriculture (USDA) accessions. SA numbers are from South Australian Research and Development Institute (SARDI) accessions. Siena refers to an accession in the 2010 seed collection list of the Botanical Museum, University of Siena, Italy (Museo Botanico, Universita’ di Siena). GB refers to University of Gothenburg herbarium. ENA refers to the European Nucleotide Archive. Chromosome counts are (1) reported from Small (2011) for the species (rather than the specific sample used here), or (2) reported in Eriksson et al. (2017) and derived from living material cultivated from USDA seeds grown at the University of Gothenburg (in parenthesis). (DOCX 16 kb

Additional file 3: Table S3. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Mean read depth and standard deviation for each accession, across all loci. (DOCX 45 kb

Supplementary Material

SUPPLEMENTARY 1., 2. Plant material and GenBank accessions for nuclear and chloroplast sequences respectively. SUPPLEMENTARY 3. Material and methods for sequencing the plant material with a description of all primers designed for this study SUPPLEMENTARY 4. Illustration of the clone filtering procedure for identifying putative PCR-recombinant sequences and cross taxon contamination. All clones for the octoploid F. mirabilis (specimen 13673) were used to construct a neighborNet (uncorrected p-distances) in SplitsTree4. From ploidal level, four distinct sequences are expected. Each group highlighted in green was composed of several nearly identical sequences and was retained for phylogenetic analysis. Red sequences, connected to the main frame of the network with zero-length terminal edges, were considered to be putative PCR recombinants and were therefore discarded. A sufficient number of clones was not recovered for the blue group, which was further investigated with clade specific primers. SUPPLEMENTARY 5. Description of the phylogenetic analyses deployed for inferring gene trees. SUPPLEMENTARY 6. Details of the BEAST analysis dating the Dicentra-Corydalis split. SUPPLEMENTARY 7. Description and results of the simulation that assessed the performance of the coalescent stochasticity test. SUPPLEMENTARY 8. Table that reports the result of the coalescent stochasticity test for the sets of sequences derived from the individual small Ne and large Ne analyses of coalescent stochasticity tests. Here, all the sequences in a set are analyzed together and the inference Ne is increased until the full set passes the coalescent stochasticity test. SUPPLEMENTARY 9. Tanglegram inferred with RAxML from sequences of the primary set. Nuclear (a) and chloroplast (b) topologies correspondences were visualized in Dendroscope 3 (Huson and Scornavacca 2012). SUPPLEMENTARY 10. Genome tree inferred with BEAST. The maximum clade credibility chronogram was built from all nuclear homoeologues (except sequences from F. bastardii), together with chloroplast haplotypes from the primary set plus those that passed the substitution model error test. PP ≥ 0.70 are indicated below branches. Icons indicate the chloroplast sequences that were added to the analysis at the different steps of genome tree reconstruction

Chloroplast alignment Supplementary Figure 10.

Chloroplast alignment used for constructing BEAST phylogeny in Supplementary Figure 10

Nuclear alignment for Figures 5, 6 and Supplementary Figure 10

Nuclear alignment used for Figures 5, 6 (STEM analyses )and Supplementary Figure 10 (BEAST analysis

The 50 loci proposed with the respective linkage group, gene reference in Mt3.0 annotation, captured portion of the gene (bp positions in the reference sequence), alignment length, substitution rate ([subst./site/year] E-9),G-C content, number and % of parsimony-informative (PI) sites, % of exon based on the reference sequence, Consistency index (CI) and Retention index (RI).

<p>The 50 loci proposed with the respective linkage group, gene reference in Mt3.0 annotation, captured portion of the gene (bp positions in the reference sequence), alignment length, substitution rate ([subst./site/year] E-9),G-C content, number and % of parsimony-informative (PI) sites, % of exon based on the reference sequence, Consistency index (CI) and Retention index (RI).</p

Frequency of recovery of each gene-tree topology across 50 genes and proportion of trees with bootstrap support greater than 80%.

<p>Frequency of recovery of each gene-tree topology across 50 genes and proportion of trees with bootstrap support greater than 80%.</p