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The largest block conserved among the three species spans more than 31 kb and includes 46 genes appearing in the same order, encoded on the same strands (ycf33, trnI, trnS.rpoC1, rpoC2, rps2).
A ~6.5 kb center to center distance is seen between both GGA25_scale1 and 3; and GGA25_scale2 and 4, which are the coding regions found on the same strands.
Most mRNA-lncRNA pairs had sense/antisense relationships, and miRNA-lncRNA pairs were prone to be located on the same strands (Table S3).
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In case of multiple genes, the host gene assigned was the one on the same strand as the miRNA.
Two CDS were phage related and all genes but one were located on the same strand.
A gene was considered active if it had at least one CAGE cluster on the same strand and within 10 bp from the TSS.
The mitogenome of A. inferum contained 13 protein-coding genes, of which one reading-frame overlapped on the same strand (atp8 and atp6 shared 7 nucleotides).
Based on the genomic coordinates, we defined small RNA clusters on the genome, where sequences overlapping on the same strand with at least one base pair are merged.
Clusters were defined as groups of microRNAs residing on the same strand within a 10 kb distance from one another.
The ambiguous reads in Fig. 3c are those reads mapped to overlapping gene regions, either on the same strand or from the opposite strands.
The rest (4 M) fell into either one of these categories: reads without a mapped mate pair, mate is mapped on the same strand or mates overlap.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com