Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Table 2

cpDNA sizes and S-IR frequencies and lengths.

Group name	Number of seq.	Median size [bp]	Shortest sequence	Longest sequence	IR/kbp; Mean; range	Longest S-IR for 50% of seq. [bp]
Euglenozoa	9	91,616	Monomorphina aenigmatica	Euglena gracilis	68	18
			(74,746 bp)	(143,171 bp)	56 – 79
Stramenopiles	37	122,660	Aureococcus anophagefferens	Cylindrotheca closterium	57	25
			(89,599 bp)	(165,809 bp)	43 – 69
Rhodophyta	60	171,284	Cyanidioschyzon merolae	Bulboplastis apyrenoidosa	59	19
			(149,987 bp)	(610,063 bp)	34 -83
Chlorophyta	90	157,916	Ostreococcus tauri	Floydiella terrestris	61	27
			(71,666 bp)	(521,168 bp)	27 – 102
Zygnemophyceae	11	142,017	Spirogyra maxima	Cosmarium botrytis	51	24
			(129,954 bp)	(207,850 bp)	32 – 64
Bryophyta	8	123,868	Syntrichia ruralis	Takakia lepidozioides	67	32
			(122,630 bp)	(149,016 bp)	44 – 78
Polypodiopsida	49	151,126	Diplazium unilobum	Lygodium japonicum	38	18
			(127,840 bp)	(157,260 bp)	34 – 52
Acrogymnospermae	85	127,659	Cathaya argyrophylla	Macrozamia mountperriensis	44	23
			(107,122 bp)	(166,341 bp)	38 – 50
Basal magnoliophyta	13	159,881	Schisandra chinensis	Trithuria inconspicua	40	18
			(146,859 bp)	(165,389 bp)	38 – 42
Magnoliidae	41	159,443	Cassytha filiformis	Piper kadsura	40	18
			(114,622 bp)	(161,486 bp)	39 – 43
Alismatales	14	163,856	Zostera marina	Wolffiella ryophyte	46	22
			(143,877 bp)	(169,337 bp)	40 – 50
Dioscoreales	10	154,205	Burmannia oblonga	Tacca leontopetaloides	47	22
			(39,386 bp)	(162,477 bp)	42 – 63
Liliales	41	152,677	Amana wanzhensis	Heloniopsis tubiflora	45	18
			(150,576 bp)	(158,229 bp)	42 – 46
Asparagales	125	153,953	Oberonia japonica	Cypripedium formosanum	44	24
			(142,996 bp)	(178,131 bp)	42 – 64
Commelinids	290	139,171	Aegilops cylindrica	Carex neurocarpa	41	17
			(113,490 bp)	(181,397 bp)	38 – 52
Early-diverging eudicotyledons	49	157,817	Kingdonia uniflora	Berberis koreana	42	19
			(147,378 bp)	(166,758 bp)	39 – 45
Santalales	9	128,744	Schoepfia jasminodora	Erythropalum scandens	45	18
			(118,743 bp)	(156,154 bp)	41 – 48
Saxifragales	10	152,692	Phedimus takesimensis	Liquidambar formosana	41	20
			(147,048 bp)	(160,410 bp)	40 – 43
Caryophyllales	32	151,686	Carnegiea gigantea	Drosera rotundifolia	45	19
			(113,064 bp)	(192,912 bp)	40 – 47
Asterids	398	153,377	Monotropa hypopitys	Adenophora divaricata	43	19
			(35,336 bp)	(176,331 bp)	38 – 61
Rosids	522	159,441	Cytinus hypocistis	Pelargonium transvaalense	45	20
			(19,400 bp)	(242,575 bp)	35 – 75
Rest	662	155,196	Pilostyles aethiopica	Pleodorina starrii	46	20
			(11,348)	(269,857)	28 – 192