Additional file 8: Table S7. of Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

Differential representation of Taxa in AA genome cultivated vs wild rhizosphere. (XLSX 66.0 kb

Transcription results of 2 putative hexose transporters of <i>C. utilis</i>.

<p>Transcription results of 2 putative hexose transporters of <i>C. utilis</i>.</p

Antisense transcripts of <i>C. utilis ADH1</i> (cut01g0000110) differentially expressed between log- and stationary-phases.

<p>Expressions at the <i>ADH1</i> locus was visualized using the Genaris integrated Next-Generation Sequencing Data Analysis Platform (GiNeS) (Genaris, Inc., Kanagawa, Japan).</p

Genome sequencing overview.

<p>Genome sequencing overview.</p

Phylogenetic tree of nitrate assimilation related genes.

<p>This tree was built on concatenated homologous sequences of all three genes (nitrate/nitrite transporter, nitrate reductases, and nitrite reductase) in Ascomycota and Basidiomycota from the subkingdom Dikarya (Materials and Methods) by the ML method.</p

<i>C. utilis</i> ADH and ALD genes, and transcription results.

*<p>Protein localization site was predicted by WoLF PSORT <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037226#pone.0037226-Horton1" target="_blank">[34]</a>.</p><p>Cyto.: Cytoplasm, Mito.: Mitochondrion.</p

Positive selection of <i>slit1</i>, <i>slit3</i>, <i>robo1</i> and <i>robo2</i> in vertebrates.

<p>(A–D) Phylogenetic trees of <i>slit1</i> (A), <i>slit3</i> (B), <i>robo1</i> (C) and <i>robo2</i> (D). All of these genes under positive selection were detected along the teleost lineages. The ω values of sites under positive selection were marked along the teleost lineage. a, b, c and d indicated the teleost lineage. Taxa names are abbreviated with the first letter of the genus and the first three letters of the species. (E) Mapping positively selected sites identified in <i>slit1</i> (black bars) and <i>slit3</i> (red bars) to domain structures of Slit. (F) Mapping positively selected sites identified in <i>robo1</i> (black bars) and <i>robo2</i> (red bars) to domain structures of Robo.</p

Positive selection of <i>slit</i> and <i>robo1</i> in insects.

<p>(A and B) Phylogenetic trees of <i>slit</i> (A) and <i>robo1</i> (B) in insects. Both of <i>slit</i> and <i>robo1</i> under positive selection were detected along the mosquito lineage. The ω values for sites under positive selection along the mosquito lineage were marked. a and b indicate the mosquito lineage. Taxa names are abbreviated with the first letter of the genus and the first three letters of the species. (C and D) Mapping positively selected sites to the Slit (C) and Robo1 (D) proteins.</p

Analysis of interacting amino acids between Slit and Robo.

<p>(A) A schematic presentation of the interaction between hSlit2 and hRobo1 through LRR2 domain (orange) bound to Ig1 domain (green) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094970#pone.0094970-Morlot1" target="_blank">[20]</a>. (B) The binding sites of hSlit2 and hRobo1 identified by SPR spectroscopy <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094970#pone.0094970-Morlot1" target="_blank">[20]</a>. (C) Phylogenetic distribution of interacting amino acids of Slit and Robo.</p

Pearson's correlation coefficient of evolutionary distances between Slit and Robo in vertebrates.

<p>**the correlation value of Slit-Robo pair is significantly different from controls at 0.01 level.</p