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

Relationship between the m⁶A methlylation extent and the transcript level in the chloroplast/amyloplast transcriptome.

<p>Relationship between the m⁶A methlylation extent and the transcript level in the chloroplast/amyloplast transcriptome.</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

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

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

Additional file 9: Table S8. of Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana

The primers used for qRT-PCR. (DOC 35 kb

Additional file 4: Table S3. of Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana

Number of m6A sites detected in the three organs of Arabidopsis. (DOC 37 kb