. 2015 Jun 9;3(6):apps.1400085. doi: 10.3732/apps.1400085

Table 3.

Amplification success prediction for the 28 fastest Shaw et al. (2014) regions.^a

Approx. Nicotiana order			Basal dicot grade/Magnoliids		Monocots				Basal eudicot grade		Eurosids I	Eurosids II	Euasterids I	Euasterids II
Approx. Nicotiana order	Genomic region	Publication^b	Amborella	Magnolia	Acorus	Cymbidium	Oryza	Canna	Ceratophyllum	Nelumbo	Fragaria	Gossypium	Olea	Helianthus	Average
1	trnH-psbA IGS												8^c
	trnH-psbA IGS	Dong et al.	NO**	NO**	NO	NO**	NO	NO	NO	NO**	NO	NO	NO	NO**	0%
	trnH-psbA IGS	Scarcelli et al.	YES	YES	YES	YES	YES	NO	YES	NO	YES	YES	YES	YES	83%
	trnH-psbA IGS	Shaw et al.	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	YES	92%
5	matK exon		12^c								6^c	12^c
	trnK (including matK)	Dong et al.	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	YES	92%
	matK exon	Scarcelli et al.	YES	YES	YES	YES*	YES	YES	YES	YES	YES	YES	YES	YES	100%
7	trnK-rps16 IGS		13^c		5^c						13^c		7^c	12^c
	trnK-rps16	Scarcelli et al.	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	YES*	92%
	trnK-3′rpS16	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
8	rps16 intron				4^c						3^c			5^c
	rps16 intron	Scarcelli et al.	YES	YES	YES	YES	YES	YES	NO	YES	NO	YES	YES	YES	83%
	rpS16 intron	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
9	rps16-trnQ IGS		2^c								11^c		1^c	13^c
	rps16-trnQ	Dong et al.	YES	YES	YES	YES	NO	NO	YES	YES	NO	NO	NO	YES	58%
	rps16-trnQ	Scarcelli et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
	5′rpS16-trnQ	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
12	trnS-trnG IGS				11^c						2^c		12^c
	trnS-trnG (and intron)	Dong et al.	NO	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	NO	75%
	trnS-trnG	Scarcelli et al.	NO	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	NO	75%
	trnS-trnG	Shaw et al.	YES	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	NO	83%
16	atpF intron										5^c
	atpF intron	Prince (here)	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
	atpF intron/exon	Scarcelli et al.	NO	YES	YES	NO	YES	YES	NO	YES	NO	YES	YES	YES	67%
18	atpH-atp IGS		9^c								12^c		4^c
	atpH-atpI	Dong et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	92%
	atpH-atpI	Prince (here)	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
	atpH-atpI	Scarcelli et al.	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	YES	92%
	atpH-atpI	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
26	rpoB-trnC IGS				8^c							10^c	11^c	7^c
	rpoB-trnC	Dong et al.	YES	YES	YES	NO	NO	NO	YES	YES	YES	YES	YES	NO	67%
	rpoB-trnC	Scarcelli et al.	NO	YES	YES	YES	YES	YES	NO	YES	YES	YES	YES	NO	75%
	rpoB-trnC	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	NO	83%
29–31	petN-psbM IGS												6^c	10^c
	petN-trnD	Scarcelli et al.	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	NO	83%
	petN-psbM	Dong et al.	NO	NO	NO	NO	NO	NO	NO	NO	NO	NO	YES	YES	17%
	ycf6-psbM	Shaw et al.	YES	YES	YES	NO	YES	NO	YES	YES	YES	YES	NO	YES	75%
32	psbM-trnD IGS		8^c		3^c							9^c
	psbM-trnD	Dong et al.	YES	YES	YES	NO	NO	YES	YES	YES	YES	YES	YES	YES	83%
	psbM-trnD	Shaw et al.	NO	NO	YES	NO	YES	YES	YES	YES	YES	YES	YES	NO	67%
33	trnE-trnT IGS											8^c		6^c
	trnD-trnT	Scarcelli et al.	YES	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	NO	83%
	trnD-trnT	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	NO	92%
34	trnT-psbD IGS		4^c								8^c	4^c		8^c
	trnT-psbD	Dong et al.	NO	YES	YES	YES	NO	YES	YES	YES	NO	YES	YES	NO	67%
	trnT-psbD	Scarcelli et al.	NO	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	83%
	trnT-psbD	Shaw et al.	YES	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	92%
38–41	psbZ-trnG IGS										7^c	2^c
	trnS-trnG	Dong et al.	YES	YES	YES	YES	NO	YES	YES	YES	YES	YES	NO	YES	83%
	trnS-trnfM	Shaw et al.	YES	YES	NO	YES	YES	YES	YES	NO	YES	NO	NO	YES	67%
	psbZ-trnfM	Scarcelli et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
50	trnT-trnL IGS		11^c		9^c							3^c
	trnT-trnL	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
55	ndhC-trnV IGS		5^c		2^c								3^c	3^c
	ndhC-trnV	Dong et al.	YES	YES	YES	YES*	YES	YES	YES	YES	YES	YES	YES	YES	100%
	ndhC-trnV	Prince (here)	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	YES	92%
	ndhC-trnV	Scarcelli et al.	YES	YES	YES	YES*	YES	YES	YES	YES	YES	YES	YES	YES	100%
	ndhC-trnV	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	YES	92%
60	atpB-rbcL IGS										9^c
	atpB-rbcL	Prince (here)	YES	YES	YES	NO	YES	YES	YES	YES	NO	NO	YES	YES	75%
	atpB-rbcL	Scarcelli et al.	NO	YES	YES	NO	YES	YES	YES	YES*	NO	YES	YES	NO	67%
62	rbcL-accD IGS				12^c								13^c
	rbcL-accD	Dong et al.	NO	YES	YES	YES	NO	YES	YES	YES	YES	YES	YES	NO	75%
	rbcL-accD	Prince (here)	YES	YES	NO	YES	NO	NO	YES	NO	NO	YES	NO	NO	42%
	rbcL-accD	Scarcelli et al.	NO	NO	NO	NO	NO	YES	NO	NO	NO	NO	NO	NO	8%
64	accD-psaI IGS		10^c		10^c
	accD-psaI	Dong et al.	NO	YES	NO	NO	NO	YES	YES	YES	YES	YES	YES	YES	67%
	accD-psaI	Prince (here)	NO	YES	NO	YES	NO	YES	YES	YES	YES	YES	YES	NO	67%
	accD-psaI	Scarcelli et al.	NO	YES	NO	YES	NO	YES	NO	YES	NO	YES	YES	YES	58%
	accD-psaI	Shaw et al.	YES	YES	NO	YES	NO	NO	YES	YES	YES	YES	YES	YES	75%
67	ycf4-cemA (ycf10) IGS											11^c
	ycf4-ycf10	Prince (here)	YES	YES	YES	YES	YES	NO	NO	YES	NO	YES	YES	YES	75%
70	petA-psbJ IGS		6^c		6^c							5^c	5^c
	petA-psbJ	Dong et al.	YES	YES	YES	NO	NO	YES	YES	YES	YES	YES	YES	NO	75%
	petA-psbJ	Prince (here)	YES	YES	YES	NO	YES	NO	YES	YES	YES	NO	NO	YES	67%
	petA-psbJ	Shaw et al.	YES	YES	YES	NO	YES	YES	YES	YES	NO	NO	YES	YES	75%
72	psbE-petL IGS		7^c		7^c						4^c	13^c		9^c
	psbE-petL	Dong et al.	NO	NO	NO	YES*	NO	YES	YES	NO	YES	NO	YES	YES	50%
	psbE-petL	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	100%
76, 77	psaJ-rpl33 IGS				13^c
	trnP-rps18	Scarcelli et al.	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	YES	NO	92%
	psaJ-rpL20	Prince (here)	NO	YES	NO	NO	NO	YES	YES	YES	NO	YES	YES	YES	58%
116	ndhF-rpl32 IGS		3^c		1^c							1^c	9^c	2^c
	ndhF-rpl32	Scarcelli et al.	YES	YES	YES	YES	YES	NO	YES	YES	YES	NO	YES	YES	83%
	ndhF-rpl32	Shaw et al.	NO	YES	YES	YES	NO	NO	NO	YES	YES	YES	YES	YES	67%
118	rpl32-trnL IGS		1^c									6^c	2^c	1^c
	rpL32-trnL	Dong et al.	NO	YES	YES	NO	YES	YES	YES	YES	YES	YES	YES	YES	83%
	rpL32-trnL	Shaw et al.	YES	YES	YES	YES	YES	YES	YES	YES	NO	YES	YES	YES	92%
121.5	ndhD-psaC IGS										10^c
127	ndhA intron										1^c		10^c	11^c
	ndhA intron	Dong et al.	NO	NO	NO	YES*	YES	NO	NO	NO	NO	YES	NO	NO	25%
	ndhA intron	Scarcelli et al.	YES	YES	YES	YES*	YES	YES	YES	YES	YES	YES	YES	YES	100%
	ndhA intron	Shaw et al.	YES	YES	YES	YES*	NO	YES	YES	YES	YES	YES	YES	YES	92%
129	rps15-ycf1 IGS											7^c		4^c
	rpS15-ycf1	Prince (here)	YES	YES	YES	NO	NO	YES	YES	YES	YES	YES	YES	YES	83%
	rps15-ycf1	Scarcelli et al.	YES	NO	YES	YES	NO	YES	YES	NO	YES	YES	NO	YES	67%

YES* = will not work for at least one species in the genus; NO** = will work if psbA primer is synthesized with one fewer A at the 3′ end.

Shaw et al., 2005, 2007; Scarcelli et al., 2011; Dong et al., 2012.

Shaw et al. (2014) rank for the region within the specified taxonomic group.