Table 1.

The Frequency of Existing Chloroplast Genome Haplotypes from 61 Species

Division	Order	Species	Size (bp)	LSC (bp)	SSC (bp)	IR (bp)	HA	HB	Frequency	P value
Angiospermae	Poales	Andropogon gerardii	139,712	81,548	12,592	22,786	31	31	0.50	1.00
		Brachypodium mexicanum a	∼135,199	∼79,447	∼12,668	∼21,542	403	373	0.52	0.30
		Eleusine coracana a	∼135,151	∼80,667	∼12,646	∼20,919	14	11	0.56	0.69
		Hordeum vulgare	136,462	81,671	12,701	21,045	347	329	0.51	0.51
		Oropetium thomaeum a	∼133,880	∼79,181	∼12,591	∼21,054	27	28	0.49	1.00
		Oryza coarctata	134,750	80,816	12,334	20,800	40	38	0.51	0.91
		Oryza longistaminata	134,567	80,596	12,357	20,807	8	4	0.67	0.39
		Oryza meyeriana	136,133	81,832	12,499	20,901	5	5	0.50	1.00
		Panicum miliaceum	140,048	81,841	9,603	24,302	37	22	0.63	0.07
		Saccharum officinarum	141,176	83,046	12,540	22,795	51	56	0.48	0.70
		Saccharum spontaneum	141,168	83,046	12,544	22,789	25	28	0.47	0.78
		Sorghum bicolor	140,754	83,733	12,503	22,259	94	71	0.57	0.09
		Zea mays	140,384	82,352	12,536	22,748	564	555	0.50	0.30
		Zoysia japonica	135,854	81,348	12,582	20,962	35	54	0.39	0.06
	Zingiberales	Musa schizocarpa a	∼169,503	∼87,828	∼11,487	∼35,094	192	210	0.48	0.40
	Asparagales	Yucca aloifolia a	∼157,785	∼86135	∼18,292	∼26,679	87	105	0.45	0.22
		Yucca filamentosa	157,785	86,135	18,292	26,679	200	202	0.50	0.96
	Ranunculales	Papaver somniferum	152,931	83,029	17,920	25,991	12	13	0.48	1.00
	Ericales	Actinidia eriantha	156,964	88,759	20,541	23,832	122	94	0.56	0.11
	Lamiales	Osmanthus fragrans	155,326	86,564	17,370	25,696	65	63	0.51	0.93
		Salvia splendens a	∼153,995	∼84,573	∼17,590	∼25,916	15	11	0.58	0.56
	Solanales	Cuscuta campestris	86,749	50,978	7,063	14,354	5	8	0.38	0.58
		Nicotiana attenuata	155,886	86,602	18,518	25,383	3	6	0.33	0.51
	Asterales	Lactuca sativa	152,765	84,103	18,596	25,033	39	31	0.56	0.40
	Cucurbitales	Siraitia grosvenorii	158,757	87,625	18,556	26,288	5	4	0.56	1.00
	Fabales	Ammopiptanthus nanus	154,084	84,070	18,014	26,000	31	43	0.42	0.24
		Arachis hypogaea	156,391	85,946	18,797	25,824	17	17	0.50	1.00
		Vigna unguiculata	152,415	81,822	17,425	26,584	4	3	0.43	1.00
	Malpighiales	Populus trichocarpa	157,033	85,129	16,600	27,652	58	78	0.39	0.40
		Salix purpurea	155,590	84,454	16,220	27,458	41	47	0.47	0.59
	Rosales	Fragaria vesca	155,691	85,606	18,173	25,956	31	25	0.55	0.51
		Fragaria ananassa	155,549	85,532	18,145	25,936	4	2	0.67	0.69
		Prunus avium a	∼157,859	∼85,977	∼19,120	∼26,381	114	128	0.47	0.40
		Rosa chinensis	156,546	85,727	18,754	26,030	5	4	0.56	1.00
		Rubus occidentalis a	∼155,760	∼85,430	∼18,768	∼25,781	9	7	0.56	0.80
	Fagales	Betula pendula	161,147	89,428	19,607	26,056	22	16	0.58	0.42
	Brassicales	Arabidopsis thaliana	154,478	84,170	17,780	26,264	135	150	0.47	0.41
		Brassica napus	152,860	83,030	17,760	26,035	51	38	0.57	0.20
		Brassica oleracea	153,364	83,136	17,834	26,197	1,714	1,773	0.49	0.33
		Brassica rapa	153,483	83,282	17,775	26,213	1,097	1,077	0.51	0.68
	Malvales	Bombax ceiba	158,997	89,022	21,111	24,432	71	96	0.43	0.06
		Gossypium arboreum	160,230	88,722	20,274	25,617	38	47	0.45	0.39
		Gossypium barbadense	160,317	88,841	20,294	25,591	11	14	0.44	0.69
		Gossypium bickii	159,422	88,073	20,183	25,583	333	330	0.50	0.94
		Gossypium darwinii	160,378	88,906	20,266	25,603	93	95	0.49	0.94
		Gossypium hirsutum	160,301	88,817	20,280	25,602	623	586	0.52	0.30
		Gossypium longicalyx	160,241	88,667	20,278	25,648	205	213	0.49	0.73
		Gossypium mustelinum	160,313	88,824	20,271	25,609	50	52	0.49	0.92
		Gossypium raimondii	160,161	88,654	20,205	25,651	48	38	0.56	0.33
		Gossypium tomentosum	160,433	88,932	20,273	25,614	42	61	0.41	0.08
		Theobroma cacao	160,619	89,333	20,194	25,546	86	77	0.52	0.53
	Myrtales	Eucalyptus albens a	∼160,076	∼88,828	∼18,476	∼26,386	20	25	0.44	0.55
		Eucalyptus marginata	160,076	88,828	18,476	26,386	13	16	0.45	0.71
		Eucalyptus melliodora	160,386	89,073	18,557	26,378	371	373	0.50	0.97
		Eucalyptus pauciflora	159,942	88,787	18,421	26,367	1,431	1,459	0.50	0.62
		Branch tip A					101	110	0.48	0.63
		Branch tip B					186	184	0.50	0.96
		Branch tip C					203	191	0.51	0.58
		Branch tip D					132	114	0.54	0.28
		Branch tip E					186	189	0.50	0.92
		Branch tip F					234	255	0.48	0.37
		Branch tip G					141	150	0.48	0.64
		Branch tip H					248	266	0.48	0.45
	Sapindales	Acer yangbiense a	∼156,262	∼86,018	∼18,072	∼26,086	104	94	0.53	0.52
		Citrus maxima	160,133	87,739	18,395	26,999	2	6	0.25	0.29
		Xanthoceras sorbifolium	161,231	85,299	18,692	28,620	110	119	0.48	0.60
Gymnosperm	Pinales	Pinus taeda	121,530	66,444	54,288	399	0	898	0.00	2.2e-16b
		Picea sitchensis	124,049	67,411	55,758	440	0	2,845	0.00	2.2e-16b
Pteridophytes	Selaginellales	Selaginella tamariscina c	126,399	53,176	47,573	12,825	0	0	—	—

^aThe long-reads were mapped to the chloroplast genome from the same genius species due to the lack of chloroplast genome of this species, so the lengths of LSC, SSC, and IR are around (∼).

^b P value ≤0.05.

^c Selaginella tamariscina only present one haplotype, haplotype C, with 174 counts, and P value is 2.2e-16.

Size, the chloroplast genome size; HA/B, haplotype A/B, the number of supported reads of LSC and SSC having identical/opposite orientation; frequency, the proportion of the count of haplotype A in the count of haplotype A + B.