Screenshots from the IGV visualized program present m⁶A topologies in rRNA and tRNAs in the <i>Arabidopsis</i> mitochondria.

<p>Extent of m⁶A methylation, sequencing depth, sequencing fragment alignment, and gene ID of the sequencing data can be clearly visualized by the IGV program [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185612#pone.0185612.ref042" target="_blank">42</a>]. The area in the screenshot indicated by the arrow, “Red leftwards arrow”, presents m⁶A methylation extent across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow”, presents sequencing fragment alignment across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow with tail”, presents gene ID information including gene ID, sequence reading direction, the intron and exon regions. (a) The whole rRNA was highly methylated by m⁶A, representative rRNA, ‘ATMG01390’; (b) The whole tRNA was slightly methylated by m⁶A, representative tRNA, ‘ATMG00380’, expressed for tRNA-Asn. The Trace files of three organs, leaves (the upper), flowers (in the middle) and roots (the lower) were presented within a screenshot.</p

The transcripts presenting extensive high m⁶A methylation in the <i>Arabidopsis</i> mitochondria.

<p>The transcripts presenting extensive high m⁶A methylation in the <i>Arabidopsis</i> mitochondria.</p

Three groupings of the m⁶A methlylation extent compared to the transcript level in the chloroplast/amyloplast transcriptome of three organs in <i>Arabidopsis</i>.

<p>Three groupings of the m⁶A methlylation extent compared to the transcript level in the chloroplast/amyloplast transcriptome of three organs in <i>Arabidopsis</i>.</p

The transcripts presenting differential transcript level and differential m⁶A methylation in the mitochondria among three organs in <i>Arabidopsis</i> (fold change >2 or <0.5, FDR < 0.02).

<p>The transcripts presenting differential transcript level and differential m⁶A methylation in the mitochondria among three organs in <i>Arabidopsis</i> (fold change >2 or <0.5, FDR < 0.02).</p

Number of the overlapped m⁶A transcripts in the two m⁶A-seq replicates.

<p>(a) in the leaf chloroplast; (b) in the flower chloroplast; (c) in the root amyloplast; (d)in the leaf mitochondria; (e) in the flower mitochondria; and (f) in the root mitochondria.</p

Screenshots from the IGV visualized program present m⁶A topologies in rRNA and tRNAs in the <i>Arabidopsis</i> chloroplast/amyloplast.

<p>Extent of m⁶A methylation, sequencing depth, sequencing fragment alignment, and gene ID of the sequencing data can be clearly visualized by the IGV program [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185612#pone.0185612.ref042" target="_blank">42</a>]. The area in the screenshot indicated by the arrow, “Red leftwards arrow”, presents m⁶A methylation extent across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow”, presents sequencing fragment alignment across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow with tail”, presents gene ID information including gene ID, sequence reading direction, the intron and exon regions. (a) The whole rRNA was highly methylated by m⁶A, representative rRNA, ‘ATCG00920’; (b) The whole tRNA with intron was highly methylated, representative tRNA, ‘ATCG00100’; and (c) The whole tRNA without intron was highly methylated, representative tRNA, ‘ATCG00110’. The Trace files of three organs, leaves (the upper), flowers (in the middle) and roots (the lower) were presented within a screenshot.</p

Proportion of the transcribed genes methylated by m⁶A in the chloroplast/amyloplast and mitochondria.

<p>Proportion of the transcribed genes methylated by m⁶A in the chloroplast/amyloplast and mitochondria.</p

Screenshots from the IGV visualized program present two typical types of m⁶A topologies in the coding RNAs in the <i>Arabidopsis</i> chloroplast/amyloplast.

<p>Extent of m⁶A methylation, sequencing depth, sequencing fragment alignment, and gene ID of the sequencing data can be clearly visualized by the IGV program [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185612#pone.0185612.ref042" target="_blank">42</a>]. The area in the screenshot indicated by the arrow, “Red leftwards arrow”, presents m⁶A methylation extent across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow”, presents sequencing fragment alignment across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow with tail”, presents gene ID information including gene ID, sequence reading direction, the intron and exon regions. (a) Type 1 (representative gene, ‘ATCG00020’, expressed for ‘photosystem II reaction center protein A’), the whole transcript without intron was highly methylated by m⁶A; and (b) Type 2 (representative gene, ‘ATCG00130’, expressed for ‘ATPase, F0 complex, subunit B/B’), the exon was highly methylated but the intron was less methylated by m⁶A. Trace files of three organs, leaves (the upper), flowers (in the middle) and roots (the lower) were presented within a screenshot.</p

The transcripts presenting differential transcript level and differential m⁶A methylation in the chloroplast/amyloplast among three organs in <i>Arabidopsis</i> (fold change >2 or <0.5, FDR < 0.02).

<p>The transcripts presenting differential transcript level and differential m⁶A methylation in the chloroplast/amyloplast among three organs in <i>Arabidopsis</i> (fold change >2 or <0.5, FDR < 0.02).</p

Additional file 2: Figure S1. of Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana

The m6A peak and adenosine peak deduced from the HPLC-MS/MS analysis. a The relative m6A peak height (upper) and adenosine peak height (lower) in the standard sample. b The relative m6A peak height (upper) and adenosine peak height (lower) in the input sample. c The relative m6A peak height (upper) and adenosine peak height (lower) in the RIP sample. (DOC 50 kb