FIG 2.

Site-by-site query reveals the discontinuous and continuous RNA synthesis near the core TRS region. The sgmRNAs of 8 canonical genes are composed of a 5′ coleader (coleader UTR to the left of the TRS in the middle), specific ORFs, and polyA tails (right). The final nt of the query reads (−7 to +5 sites) is displayed on the horizontal axis. The site-matched return reads are aligned discontinuously with their 5′ sequences mapped to the coleader UTR and 3′ sequences aligned to probable ORFs (displayed on the vertical, including widely accepted S, ORF6, ORF7, ORF8, N, M, ORF3, and E, and truncated/mutated ORFs, including N1 and ORF7p1 to 3), except for the genomic reads (as gRNA, or ORF1), which are continuously aligned to the genome. The site-matched read counts are indicated by colored circles. The solid red outline indicates the coleader of the sgmRNAs and gRNA, which ends at the red dashed line for the reads of most sgmRNAs. The ORFs revealed by return reads of each sgmRNA are demonstrated downstream of the coleader, with coding sequences in italics. The discontinuous synthesis of N1 is indicated by a wavy line. A GAACttt sequence, underscored with a dashed line, exists upstream of the three truncated ORFs (ORF7p1 to ORF7p.3) and is a minor TRS used in noncanonical sgmRNA synthesis. The localization of their first sites relative to the stop codon of ORF7 is indicated by the superscript number with an underscore.