Fig. 2: Translational landscapes of M. incognita as defined by multi-omics data.

A Analysis workflow for novel transcript discovery and lncRNA prediction, the class codes of novel transcripts were adapted from gffcompare⁷³, class code “u”: intergenic, class code “i”: novel transcript fully contained in an annotated intron, class code “x”: exon match on the opposite strand, class code “y”: contains a reference within its introns, and class code “o”: other same strand overlap with reference exons. The transcripts with no hits against the eggNOG database were retained and subsequently filtered by LGC tool⁷⁵ and coding potential calculator (CPC2)⁷⁶ to remove the transcripts with coding potential. B Number of actively translated ORFs identified from novel transcripts. C Proportion of actively translated ORFs identified from putative lncRNAs. D Number of actively translated ORFs identified from reference genome annotation: annotated ORFs, ORFs overlapping with annotated CDS with the same start and stop codon; internal ORFs, ORFs located within annotated CDS but in different reading frame; overlapped ORFs, ORFs located upstream or downstream of annotated CDS and overlapping with them; dORFs, ORFs located downstream of annotated CDSs but not overlapped with annotated CDSs; uORFs, the ORFs located upstream of annotated CDS but not overlapping with them. E Visualization of read coverage on actively translated ORFs at transcriptional and translational levels using Integrative Genomics Viewer (IGV).