Figure 1.
Inflorescence of O. italica after (A) and before (B) anthesis. (C) Schematic diagram of a single floret of O. italica.
Table 1.
Protein coding unigenes selected for the expression analysis validation.
Table 2.
Putative long non-coding unigenes selected for the expression analysis and nucleotide sequence of the primer pairs used in the amplification experiments.
Table 3.
Sequence assembly summary statistics.
Figure 2.
Size distributions of the assembled transcripts (A) and unigenes (B) of the inflorescence of O. italica.
The length ranges are indicated in base pairs.
Figure 3.
Size distribution of the annotated transcripts.
(A) Relationship between the sequence length of the assembled unigenes and the percentage of annotations in the NCBI nr protein database. (B) Number of annotated unigenes for each size class. The lengths are indicated in base pairs.
Table 4.
Statistics of the annotation results for the O. italica unigenes.
Figure 4.
Functional annotations of the unigenes of O. italica.
(A) Level 2 GO term distribution for the biological process, cellular component and molecular function categories. (B) KOG annotation.
Figure 5.
Transcription factor annotations of the unigenes of O. italica obtained from the plant TFDB.
Table 5.
Summary statistics of the Pfam domain annotations with occurrence >100.
Table 6.
Summary of the KEGG pathways analysis indicating the number (N) of unigenes and the number of corresponding enzyme matches.
Figure 6.
Relative expression levels of selected protein coding unigenes of O. italica assessed by real-time PCR analysis of inflorescence tissue (A) and by normalized FPKM counts (B).
Both measures were normalized relative to the actin levels. The bars indicate the standard deviation.
Figure 7.
Comparison of the level 2 GO annotations between the reference transcriptome of O. italica (blue) and the 1,144 unigenes with FPKM counts greater than 100 (red).
Asterisks indicate the significantly enriched GO terms among the most expressed unigenes (Fisher exact test p<0.05).
Figure 8.
Selected putative long non-coding RNAs expressed in the inflorescence of O. italica.
(A) Agarose gel electrophoresis of the RT-PCR-amplified products of the selected transcripts. Lane 1, comp0_c0_seq1; lane 2, comp3328_c0_seq1; lane 3, comp1231_c0_seq1; lane 4, comp3311_c0_seq1; lane 5, comp48038_c0_seq1; lane 6, comp6669_c0_seq1; lane 7, comp4129_c0_seq1; lane 8, comp1308_c0_seq1; lane 9, comp15481_c0_seq1; lane 10, comp134696_c0_seq1; lane 11, empty; lane 12, 100 bp ladder. (B–G) Relative expression level (Rn) in the outer tepals (Te_out), inner tepals (Te_inn), labellum (Lip), column (Co), ovary (Ov) and leaf (Le) of the transcripts comp0_c0_seq1 (B), comp3328_c0_seq1 (C), comp1231_c0_seq1 (D), comp48038_c0_seq1 (E), comp6669_c0_seq1, (F), and comp134696_c0_seq1 (G). The bars indicate the standard deviation.
Figure 9.
Nucleotide sequence alignment of comp134696_c0_seq1 of O. italica and the TAS3 sequences of Hordeum vulgare (accession number BF264964), Zea mays (BE519095), Saccharum hybrid cultivar (CA145655), Sorghum bicolor (CD464142), Oryza sativa (AU100890), and Triticum aestivum (CN010916).
The 5′ and 3′ conserved sequences that are targets of miR-390 are underlined.