supplementary figures and Tables from Cultured cells and wing disc size of silkworm can be controlled by the Hippo pathway

Hippo signalling represents a cell proliferation and organ-size control pathway. Yorki (Yki), a component of the Hippo pathway, induces the transcription of a number of targets that promote cell proliferation and survival. The functions of <i>Yki</i> have been characterized in Drosophila and mammal, while there are few reports on silkworm, <i>Bombyx mori</i>. In the present study, we found that <i>BmYki3</i> facilitates cell migration and cell division, and enlarges the cultured cell and wing disc size. CoIP results indicated that BmYki3 may interact with thymosin, E3 ubiquitin-protein ligase, protein kinase ASK1, dedicator of cytokinesis protein 1, calcium-independent phospholipase A2 and beta-spectrin. RNA-seq results indicated that 4444 genes were upregulated and 10291 genes were downregulated after <i>BmYki3</i> was overexpressed in the cultured cells. GO annotation indicated that the up/downregulated genes were enriched in 268/382 GO terms (<i>p</i> < 0.01); KEGG analysis showed that the up/downregulated genes were enriched in 49/101 pathways. These findings provided novel information to understand the functions of <i>BmYki3</i> in a cell proliferation and organ-size control pathway

Heatmap and sorting analysis of the different samples.

<p>(a) Heatmap based on the hierarchical clustering solution (Bray–Curtis distance metric and complete clustering method) of the 12 samples. Rows and columns all represent the 12 samples, the similarity represented by the values in the heatmap and the heatmap of bacterial microbiota in different samples, unweighted UniFrac distance metric between samples using Unifrac was calculated to make the heatmap, the lower number represents greater similarity in bacterial microbiota between samples in the heatmap. (b) Sample sorting analysis, A PCoA plot was used to visualize the data based on β-diversity metrics of weighted UniFrac. Scatterplot of PCA-score depicting variance of fingerprints derived from different bacterial community. Principal components (PCs) 1, 2 and 3 explained 51.74%, 33.34% and 6.53% of the variance, respectively.</p

Phylogenetic trees of predominant genera in different samples.

<p>The phylogenetic tree was inferred using the neighbor-joining method with MEGA6.0 and the bootstrap value was 1000 replications. Only the branch with bootstrap value >500 are shown in the tree. (a) for CK-144-F, (b) for CK-144-M, (c) for CPV-144-F, and (d) for CPV-144-M; the numbers in parentheses represented the percentage of a predominant genus. Serial numbers from 1–12 represented the <i>Delftia</i>, <i>Pelomonas</i>, <i>Tepidimona</i>, <i>Ralstonia</i>, <i>Aspromonas</i>, <i>Pseudomonas</i>, <i>Enterococcus</i>, <i>Methylobacterium</i>, <i>Staphylococcus</i>, <i>Tepidimonas</i>, <i>Corynebacterium</i> and <i>Brevibacterium</i> genera, respectively. Samples CK (CPV)-144-F (M) were mentioned in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146313#pone.0146313.t001" target="_blank">Table 1</a>.</p

PCA analysis of the predominant genera according to their abundance in the bacterial microbiota.

<p>PCA analysis with linear ordination methods was used to explore the correlation between dominant genera using CANOCO 4.5 according to ter Braakand Šmilauer [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146313#pone.0146313.ref013" target="_blank">13</a>].</p

Shared genera analysis of the different samples.

<p>Venn diagram showing the unique and shared genera in the different samples. CK (CPV)-24(72,144)-F (M) are samples mentioned in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146313#pone.0146313.t001" target="_blank">Table 1</a>. CK-F (M)-S was a general designation of CK-24-F (M), CK-72-F (M) and CK-144-F (M). CPV-F (M)-S was a general designation of CPV-24-F (M), CPV-72-F (M) and CPV-144-F (M). (a) for CK-24-F, CK-72-F and CK-144-F samples; (b) for CK-24-M, CK-72-M and CK-144-M samples; (c) for CPV-24-F, CPV-72-F and CPV-144-F samples; (d) for CPV-24-M, CPV-72-M and CPV-144-M samples; (e) for CK-F-S, CK-M-S, CPV-F-S and CPV-M-S samples.</p

Richness rarefaction and Shannon index analysis of the different samples.

<p>CK (CPV)-24(72,144)-F (M) are samples mentioned in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146313#pone.0146313.t001" target="_blank">Table 1</a>. (a) Rarefaction curves of OTUs clustered at 97% sequence identity across difference samples. (b) Rarefaction curves of the Shannon index according to OTU. Shannon indices approached a plateau and the rarefaction curves showed it ranged from 6 to 9.</p