Fig. 4

Alternatively spliced isoforms and polycistronic PKS gene expression in Amphidinium gibbosum. a AS events and their frequencies. SE “skipped exon,” RI “retained intron,” MXE “mutually exclusive exon,” and A3SS and A5SS “alternative 3′ and 5′ splice events”. Black boxes indicate constitutively spliced exons while blue boxes represent alternatively spliced exons. b Gene ontology (GO) biological processes showing significant enrichment of all genes undergoing alternative splicing. c Alternative 3′ splice sites (i) and skipped exons (ii) were identified on a ketosynthase gene (g70808) on scaffold 13486. Phosphate and nitrate experiments are shown in red while controls are in orange. Expression is plotted on the y-axis, genomic coordinates on the x-axis, and isoforms are at bottom in black, with exons depicted in black boxes. Read coverage is represented with numbers. d Sashimi plot showing three uni-directionally aligned PKS genes on scaffold1342 (colored in blue) with multiple polycistronic transcripts (red lines) spanning these genes. PKS module organization within genes is based on PFAM annotation. Iso-Seq read coverage is represented by red vertical blocks, and splicing junction support is shown with numbers. Exons are shown in blue blocks, and lines between blue blocks represent introns. KS "ketosynthase," DH "dehydratase," ER "enoylreductase," KR "ketoreductase"