Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data

Table 3 Comparison of intron annotation between automated predictions and Iso-seq alignment of chloroplast genes in C. lentillifera

Intron contained genes	Number of introns			Putative intron type ^c
Intron contained genes	Iso-seq data	FMannot	Geseq	Putative intron type ^c
rrn16	3	0	0	Intron 1: undetermined (LHE) Intron 2: undetermined (LHE) Intron 3: undetermined (LHE)
rrn23	5	0	0	Intron 1: group I Intron 2: group I Intron 3: group I Intron 4: group I Intron 5: undetermined (LHE)
psbA	4	4	4^a	Intron 1: group II Intron 2: group II Intron 3: group I Intron 4: group II
psbD	1	1	1	Intron 1: group I
rbcL	1	1	1	Intron 1: group II
atpF ^b	1	0	0	Intron 1: non-canonical group II (derived domain V)
ccsA ^b	1	0	0	Intron 1: non-canonical group II
rpoC2	0	0	1	–
rpoC1	0	0	1	–

^a Boundaries of psbA intron 2 cannot be accurately predicted
^b atpF and ccsA were mis-predicted by FMannot and Geseq
^c Introns of atpF and ccsA were classified as non-canonical group II intron here, because they have conserved or derived domain V but lack of typical exon-intron boundaries and intronic ORFs of group II intron. LHE indicates a LAGLIDADG homing endonuclease domain within the intron

ISSN: 1471-2164