Table 1.

Gene order and sequence difference among Scirtothrips dorsalis South Asia 1 (SA1) and East Asia 1 (EA1) cryptic species

SA1	Stranda	EA1	Stranda	Sequence differenceb
cox1	J	cox1	J	11.76 %
nad3	J	nad3	J	19.21 %
L 2	J	L 2	J	5.97 %
cox2	J	cox2	J	12.83 %
D	J	D	J	13.43 %
R	J	R	J	1.47 %
	J	Non-coding	J	Non-homologous
G	J	G	J	9.23 %
K	J	K	J	4.76 %
cox3	J	cox3	J	11.28 %
I	J	I	J	14.29 %
L 1	J	L 1	J	9.23 %
T	J	T	J	7.81 %
P	J	P	J	9.23 %
N	J	N	J	10.17 %
E	J	E	J	12.12 %
Q	J	Q	J	2.94 %
cob	J	cob	J	13.51 %
Y	J	Y	N	10.61 %
nad2	J	nad2	J	19.64 %
W	J	W	J	7.35 %
nad1	J	nad1	J	17.80 %
M	J	M	J	6.25 %
A	J	A	J	3.03 %
F	N	F	J	4.41 %
rrnS	J	rrnS	J	12.42 %
atp8	J	atp8	J	21.14 %
atp6	J	atp6	J	18.82 %
S 1	J	S 1	J	11.67 %
Control	J	Control	J	29.15 %
nad5	N	nad5	N	16.34 %
Non-coding	N		N	Non-homologous
H	N	H	N	15.15 %
nad4	N	nad4	N	19.12 %
nad4L	N	nad4L	N	20.63 %
C	J	C	J	8.06 %
nad6	J	nad6	J	21.37 %
V	J	V	J	13.33 %
rrnL	J	rrnL	J	12.09 %
S 2	J	S 2	J	4.41 %

Genomes are linearized and SA1 Chromosome 2 (bold) is inserted into its proposed ancestral location; tRNA genes are abbreviated to the letter of their coding amino acid, S ₁ (anticodon tct), S ₂ (tga), L ₁ (tag), L ₂ (taa)

^aMajority (J), Minority (N) coding strands

^bIndels were treated as a single difference regardless of size and non-overlapping regions at the termini of tRNA alignments were ignored