Fig. 1

The amounts and structures of noncanonical coronavirus transcripts in BCoV-infected HRT-18 cells based on nanopore direct RNA sequencing. A Schematic diagram of the BCoV genome structure. TRSs, including TRS-L, noncanonical TRS-B (ncTRS) and canonical TRS-B (cTRS), are denoted by solid blue rectangles. L, leader. B The amounts of BCoV transcripts in BCoV-infected HRT-18 cells based on the read counts of nanopore direct RNA sequencing. ENO2, yeast enolase II mRNA. C The amounts of BCoV transcripts based on the number of fragments of which the transcripts are composed. D The amounts of each classified BCoV transcript. E Schematic diagram showing the structures of canonical BCoV transcripts (i.e., canonical sgmRNAs). F Schematic diagram illustrating the structures of noncanonical BCoV transcripts, which are divided into 2 main populations: noncanonical sgmRNAs and defective viral genomes (DVGs) (see text for details). The data in (B–D) represent the means of two independent experiments. UTR, untranslated region; ORF, open reading frame; An, poly(A) tail; 32 K, 32 kDa protein; HE, hemagglutinin/esterase; S, spike protein; 12.7, 12.7 kDa protein; E, envelope protein; M, membrane protein; N, nucleocapsid protein; BCoV, bovine coronavirus; ENO2, enolase II; HRT-18, human rectum tumor-18 cells; DVG, defective viral genome; sgm, subgenomic mRNA; L, leader; c, canonical; nc, noncanonical; TRS, transcription regulatory sequence. ΔL_cTRS_sgm, leader-less sgmRNA derived from canonical TRS; L_ncTRS_sgm, sgmRNA derived from noncanonical TRS; ΔL_ncTRS_sgm, leader-less sgmRNA derived from noncanonical TRS; 5′3′DVG, DVG with sequence elements from 3′ UTR and 5′ UTR; Δ5′DVG, DVG with a sequence element from 3′ UTR; Δ3′DVG, DVG with a sequence element from 5′ UTR; Δ5′3′DVG, DVG lacking sequence elements from 3′ UTR and 5′ UTR