Characteristics of ra-siRNAs in <i>G</i>. <i>barbadense</i>.

<p>The length distribution of ra-siRNAs is shown in A, and the 5’first nucleotide of ra-siRNAs is shown in B. Transposon, retrotransposon, rRNA and simple repeat represent different derivations of ra-siRNAs.</p

Characteristics of Pima pha-siRNAs.

<p>The distribution of p-value for Pima PYTs is shown in A, the classification of PYTs is shown in B, and the distribution of the 5’first nucleotide is shown in C. Auxin: auxin-related transcription factors; Other TF: other transcription factors; NBS: NBS-LRR disease resistance proteins; Repeat: repeat proteins; <i>TAS3</i>: <i>Arabidopsis TAS3</i> homologs; Enzymes: various enzymes; Predicted: predicted proteins; Uncharacterized: uncharacterized proteins.</p

Bioinformatics Analysis of Small RNAs in Pima (<i>Gossypium barbadense</i> L.)

<div><p>Small RNAs (sRNAs) are ~20 to 24 nucleotide single-stranded RNAs that play crucial roles in regulation of gene expression. In plants, sRNAs are classified into microRNAs (miRNAs), repeat-associated siRNAs (ra-siRNAs), phased siRNAs (pha-siRNAs), <i>cis</i> and <i>trans</i> natural antisense transcript siRNAs (<i>cis</i>- and <i>trans</i>-nat siRNAs). Pima (<i>Gossypium barbadense</i> L.) is one of the most economically important fiber crops, producing the best and longest spinnable fiber. Although some miRNAs are profiled in Pima, little is known about siRNAs, the largest subclass of plant sRNAs. In order to profile these gene regulators in Pima, a comprehensive analysis of sRNAs was conducted by mining publicly available sRNA data, leading to identification of 678 miRNAs, 3,559,126 ra-siRNAs, 627 pha-siRNAs, 136,600 <i>cis</i>-nat siRNAs and 79,994 <i>trans</i>-nat siRNAs. The 678 miRNAs, belonging to 98 conserved and 402 lineage-specific families, were produced from 2,138 precursors, of which 297 arose from introns, exons, or intron/UTR-exon junctions of protein-coding genes. Ra-siRNAs were produced from various repeat loci, while most (97%) were yielded from retrotransposons, especially LTRs (long terminal repeats). The genes encoding auxin-signaling-related proteins, NBS-LRRs and transcription factors were major sources of pha-siRNAs, while two conserved <i>TAS</i>3 homologs were found as well. Most <i>cis</i>-NATs in Pima overlapped in enclosed and convergent orientations, while a few hybridized in divergent and coincided orientations. Most <i>cis</i>- and <i>trans</i>-nat siRNAs were produced from overlapping regions. Additionally, characteristics of length and the 5’-first nucleotide of each sRNA class were analyzed as well. Results in this study created a valuable molecular resource that would facilitate studies on mechanism of controlling gene expression.</p></div

Venn diagram shows the number of miRNAs derived from different originations.

<p>The numbers of miRNAs of Pima derived from different originations are shown in A (conserved miRNAs) and B (lineage-specific miRNAs), respectively. A2, D5 and cotton transcripts represent the number of miRNA family detected from A2 genome (<i>G</i>. <i>arbroeum)</i>, D5 genome (<i>G</i>. <i>raimondii</i>) and cotton transcripts, respectively.</p

miRNA-mediated pha-siRNA yielding pathways.

<p>Four miRNA-mediated pha-siRNAs yielding pathways are shown in A, B, C and D. The red and blue letters represent pha-siRNAs. The vertical line “|” and colon “:” represent Watson-Crick base-pairs and G-U pairs, respectively.</p

Characteristics of Pima miRNAs.

<p>The length distribution of Pima miRNAs is shown in A, and the 5’end nucleotide distribution of Pima miRNAs is shown in B.</p

Characteristics of <i>cis</i>-NATs and <i>cis</i>-nat siRNAs in Pima.

<p>The numbers of each type of <i>cis</i>-NAT orientations are shown in A. The number of <i>cis</i>-nat siRNAs detected from the A2 and D5 genome is shown in B. The length distribution of <i>cis</i>-nat siRNAs is shown in C. The 5’first nucleotide of <i>cis</i>-nat siRNAs is shown in D. The enrichment analysis of <i>cis</i>-nat siRNAs is shown in E; exon/intron, overlap/non-overlap region, and plus/minus stand represent different derivations of <i>cis</i>-nat siRNAs.</p

Additional file 4: Table S5. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

IntronR-2nd dataset. (XLSX 203 kb

Additional file 6: Table S7. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

Exonic Intron-1st & 2nd datasets. (XLSX 43 kb

Additional file 3: Table S4. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

IntronR-1st dataset. (XLSX 125 kb