ncRNAs with homology to multiple small RNAs.

<p>ncRNAs with homology to multiple small RNAs.</p

Results of genic localization for ncRNAs covering <50% of a gene model.

<p>A total of 472 ncRNAs were had homology with filtered gene set genes that covered less than 50% of the gene model. This homology spanned different genic features (A). (A). The number of sequences that aligned with a specific genic feature is indicated for each groupof ncRNAs (B). Some lncRNAs covered more than one feature of the gene (C). Within this group, those that include the upstream or downstream regions were reported separately.</p

Combination of the Python Pipeline and CPC results.

<p>The Python Pipeline and CPC were used to identify noncoding RNAs, the number of transcripts identified as noncoding by each method is indicated. A subset were classified as noncoding by both methods, others were identified exclusively by one set or the other. The sequences identified as noncoding by either method were combined into one comprehensive set (Combined ncRNA). Datasets for ncRNAs identified by the Python pipeline, CPC, and the combined set were designated <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043047#pone.0043047.s012" target="_blank">Dataset S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043047#pone.0043047.s013" target="_blank">S2</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043047#pone.0043047.s014" target="_blank">S3</a> respectively (supplementary data).</p

Results of genic localization for ncRNAs covering >98% of a gene model and spliced.

<p>A total of 541 ncRNAs were either spliced or had homology with filtered gene set genes over 98% of the gene model. This homology spanned different genic features (A). The number of sequences that aligned with a specific genic feature is indicated for each group of ncRNAs (B).</p

Homology of miRNA precursors with previously classified miRNA precursor sequences.

<p>Homology of miRNA precursors with previously classified miRNA precursor sequences.</p

Results for the classification of combined noncoding RNA datasets (ncRNAs) based on small RNA precursor potential.

<p>Long noncoding RNA candidates identified above were classified into four different subsets based on alignment with small RNA databases including microRNA sequences (miRNA), short hairpin forming RNA sequences (shRNA),small interfering RNA sequences (siRNA), and those without homology to small RNA sequences, classified as long noncoding RNAs (lncRNA).</p

Results of genic vs. intergenic localization.

<p>Each subgroup of ncRNA was localized to either a genic or intergenic region in the maize genome. The number of genic and intergenic transcripts for each class of ncRNA are indicated.</p

Known lncRNAs with ORF size in amino acids.

<p>Known lncRNAs with ORF size in amino acids.</p

Python pipeline results on 18, 668 full-length cDNAs.

<p>The starting data set for the pipeline are 18,668 full-length cDNA sequences. The sequences are sequentially analyzed for protein coding potential using ORF length and homology of predicted protein with known proteins as indications of coding potential. The full-length cDNA sequences that pass through are designated as noncoding RNAs (ncRNAs) and are contained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043047#pone.0043047.s012" target="_blank">Dataset S1</a> (supplementary data).</p

Repetitive element content of intergenic lncRNA candidates by class.

<p>Repetitive element content of intergenic lncRNA candidates by class.</p