Pollination mechanism of <i>P. parishii</i>.

<p>(<b><i>A</i></b>) Structural characteristics of the column. The distance between the anther (red arrow) and stigma (blue arrow) is 2 mm to 3 mm (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037478#pone-0037478-g001" target="_blank">Figures 1B and 1E</a>). (<b><i>B</i></b>) The flower moves backward and upward, making the both of anthers and the lateral lobes of the stigma lie in a horizontal plane, and solid-state pollinia begin to liquefy (red arrow). (<b><i>C</i></b>) The anther continues to liquefy close to the stigma and touches its margin (red arrow). (<b><i>D</i></b>) The anther liquid spreads onto the receptive surface of the stigma (red arrow). (<b><i>E</i></b>) Floral morphology and structure. The anther and stigma are shown in red and blue arrows, respectively. (<b><i>F</i></b>) Floral morphology and structure of <i>P. dianthum</i> pollinated by hoverflies. The anther and stigma are shown in red and blue arrows, respectively. (<b><i>G</i></b>) The column of <i>P. dianthum</i>, whose anthers do not liquefy (red arrow).</p

The transcriptome functional annotation

The dataset contains functional annotation and gene coding sequence annotation for 11tissues. There are five annotation files per tissues, which are three functional annotation files and two structural annotation files, respectively. They are the KEGG, COG and Nr database annotation files. The cds and pep files are fasta format, the title in the files contains unigene name predicted coding sequence, the locus and the coding directio

The transcriptome assembly

The dataset contains the unigenes from the longest contigs per transcripts generated by Trinity. The fb.flower bud.Unigene.fa file contains unigenes from flower of P. equestris, the L5.root.Unigene.fa file are unigenes from root of P. equestris, the L6.stem.Unigene.fa file contains unigenes from stem of P. equestris, the PHA.leaf. Unigene.fa file contains unigenes from leaf of P. equestris. 12_day.unigene.fasta, 7_day.unigene.fasta and 4_day.unigene.fasta files are unigenes from seeds respectively taken from sowing on 1/2 MS medium for 12 days, 7 days and 4 days. sepal.unigene.fasta, petal.unigene.fasta, lip.unigene.fasta and column.unigene.fasta files are unigenes from sepal, petal, lip and column

HSP gene family in the eleven transcriptome

We tested full-length transcripts against the HSP90 and HSP70 gene family in order to examine the completeness of the data by comparing 11 tissues transcriptomes with P. equestris genome. PEQU means P. equestri; flower bud, root, stem and leaf are labeled by fb, L5, L6 and PHA, respectively. 4_day_seed, 7_day_seed and 12_day_seed are seeds respectively taken from sowing on 1/2 MS medium for 4 days, 7 days and 12 days

Functional analysis of serial deletions of <i>PeMADS6</i> promoter.

<p>(A) Serial deletion constructs of <i>PeMADS6</i> promoter. (B-Q) Histochemical assay of flower organs bombarded with serial deletions of <i>PeMADS6</i> promoter shown in the order of pBI-Pe6p-1108 (B–E), pBI-Pe6p-808 (F–I), pBI-Pe6p-508 (J–M) and pBI-Pe6p-208 (N–Q). Constructs were bombarded into four independent floral buds, and results are representative of three independent bombardment experiments. Scale bar  = 0.5 mm. (R) Dual luciferase assay of serial deletions of <i>PeMADS6</i> promoter. The same letters above the bars are not statistically different by T-test analysis (p<0.01). Data are mean ± SD (<i>n</i> = 6). All constructs were analyzed for promoter activities of driving luciferase expression by bombardment into two floral buds, and results are representative of three independent bombardment experiments.</p

P. equestris genome functional annotation

The P. equestris genome function annotation dataset contains the blast results from KEGG, InterPro, Swissprot, TrEMBL databas

Promoter sequences of <i>PeMADS2∼6</i> and the putative CArG boxes.

<p>Length of promoter sequences of <i>PeMADS2, PeMADS3</i>, and <i>PeMADS6</i> were 3,249, 1,293 and 1,514 bp, respectively. The promoter sequence of the <i>PeMADS4</i> was extended from −422 bp to −3,303 bp (horizontal line box), and the original fragment of −2,121 to −840 bp of <i>PeMADS5</i> promoter was replaced by a 1,227-bp fragment (diagonal line box). The rhombus and the triangles indicate the putative CArG boxes predicted by consensus CC(A/T)₆GG and C(A/T)₈G motifs, respectively. “+1” means the transcription start site and ATG was the translation start site. The lengths of the promoters are show from the transcription start site to the upstream sequences.</p

Histone Acetylation Accompanied with Promoter Sequences Displaying Differential Expression Profiles of B-Class MADS-Box Genes for <i>Phalaenopsis</i> Floral Morphogenesis

<div><p>Five B-class MADS-box genes, including four <i>APETALA3</i> (<i>AP3</i>)-like <i>PeMADS2</i>∼<i>5</i> and one <i>PISTILLATA</i> (<i>PI</i>)-like <i>PeMADS6</i>, specify the spectacular flower morphology in orchids. The <i>PI</i>-like <i>PeMADS6</i> ubiquitously expresses in all floral organs. The four <i>AP3</i>-like genes, resulted from two duplication events, express ubiquitously at floral primordia and early floral organ stages, but show distinct expression profiles at late floral organ primordia and floral bud stages. Here, we isolated the upstream sequences of <i>PeMADS2∼6</i> and studied the regulatory mechanism for their distinct gene expression. Phylogenetic footprinting analysis of the 1.3-kb upstream sequences of <i>AP3</i>-like <i>PeMADS2</i>∼<i>5</i> showed that their promoter regions have sufficiently diverged and contributed to their subfunctionalization. The amplified promoter sequences of <i>PeMADS2</i>∼<i>6</i> could drive <i>beta-glucuronidase</i> (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage. The promoter sequence of <i>PeMADS4</i>, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal. Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of <i>PeMADS4</i> in lip as compared in petal. All these results suggest that the regulation via the upstream sequences and increased H3K9K14ac level may act synergistically to display distinct expression profiles of the <i>AP3</i>-like genes at late floral organ primordia stage for <i>Phalaenopsis</i> floral morphogenesis.</p></div

P. equestris genome assembly

The P. equestris genome scaffolds and the file containing the locational relationship between the superscaffold and scaffolds or contig

GUS histochemical staining for the promoter activities of <i>PeMADS2</i>∼<i>6</i>.

<p>Histochemical assay of GUS expression in floral organs shown in the order of pBI-Pe2p-3249 (A–D), pBI-Pe3p-1293 (E–H), pBI-Pe4p-3303 (I–L), pBI-Pe5p-2062 (M–P), pBI-Pe6p-1514 (Q–T), pBI221 (U–X) and pBI-PL (Y-AB). Constructs were bombarded into four independent floral buds, and results are representative of three independent bombardment experiments. Scale bar  =  0.5 mm.</p