Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors

Table 1 RNA editing patterns in the chloroplast ndhD gene of the selected early branching angiosperms Amborella trichopoda, Calycanthus floridus, Ceratophyllum demersum, Chloranthus spicatus, Illicium oligandrum, Liriodendron tulipifera, Magnolia kwangsiensis, Nuphar advena and Zingiber spectabile in comparison to the ones of Arabidopsis thaliana and Cucumis sativus

	Amborella trichopoda	Calycanthus floridus	Ceratophyllum demersum	Chloranthus spicatus	Illicium oligandrum	Liriodendron tulipifera	Magnolia kwangsiensis	Nuphar advena	Zingiber spectabile	Arabidopsis thaliana	Cucumis sativus
eU2TM	ed	ed	ed	ed	ed	ed	ed	ed	ed	ed	ed
eU59SL	ed	ed	ed	ed	ed	ed	ed	p	C	p	p
eU145HY	p	p	p	p	p	p	p	p	ed	p	p
eU239PL	p	ed	p	p	p	p	p	p	p	M	p
eU305SL	ed	p	p	p	p	p	p	ed	p	p	p
eU313RW	p	ed	p	ed	p	ed	ed	ed	p	F	p
eU383SL	ed	ed	p	ed	ed	ed	ed	p	ed	ed	ed
eU548SL	p	ed	p	ed	ed	ed	ed	p	p	p	p
eU599SL	ed	p	ed	ed	p	ed	ed	p	p	p	ed
eU668AV	ed	p	p	p	ed	p	p	p	p	p	p
eU674SL*	ed	ed	p	ed	ed	ed	p	ed	p	ed	ed
eU878SL	ed	ed	ed	ed	ed	ed	ed	ed	ed	ed	ed
eU887PL*	p	p	p	ed	ed	ed	ed	p	ed	ed	ed
eU944SF	ed	p	p	p	p	p	p	p	p	p	p
eU947TI	ed	ed	p	p	p	ed	ed	p	ed	p	p
eU1163SL	ed	p	p	p	p	p	p	p	p	p	p
eU1193SL	F	p	p	ed	ed	ed	ed	p	ed	p	p
eU1298SL	p	ed	ed	ed	ed	ed	ed	ed	p	p	p
eU1310SL	ed	p	p	ed	ed	ed	ed	ed	p	p	p
eU1424TI	p	p	p	p	p	p	p	p	ed	p	p
18 + 2	12	10	5	12	11	13	12	7	8	5	6

A ‘p’ indicates a pre-edited status, i.e. a thymidine on DNA level. Editing nearly always restores universally conserved amino acids except for a cysteine (C) in Zingiber corresponding to ndhDeU59SL, a methionine (M) in Arabidopsis in position ndhDeU239PL and phenylalanines (F) in Arabidopsis in position ndhDeU313RW and in Amborella in position ndhDeU1193SL. Editing (ed in bold) has been investigated in this study except for Ceratophyllum and Zingiber (predictions only) and for Arabidopsis and Cucumis where it was analyzed previously. Editing events eU674SL and eU887PL labelled with asterisks may cause alternative codon changes (PL, SL, SF) in some taxa

ISSN: 2730-7182