Table 1.

Identity of the Chloroplast Genome of Several citrus and Citrus-Related Species Inferred from the Chloroplast DNA Sequence.

Species	Cultivar	Chloroplast Genome	SNVs	Indels	Mapped Reads	Mean Coverage	Genome Fraction > 15×
Citrus sinensis	Sweet orange	PU	0a	0b	4,794,814	2,097	100.0
Citrus aurantium	Sour orange	PU	16	04	20,959,168	9,078	100.0
Citrus limon	Eureka lemon	PU	16	04	7,913,464	3,410	100.0
Citrus maxima	Chandler pummelo	PU	18	01	2,817,860	1,283	100.0
Citrus paradisi	Marsh grapefruit	PU	18	01	7,090,516	3,049	100.0
Citrus grandis	Low acid pummelo	PU	18	01	1,305,264	577	99.9
Citrus grandis	Guanxi pummeloc	PU	18	01	2,779,065	1,302	98.5
Citrus grandis	Shatian pummeloc	PU	18	01	3,121,627	1,462	99.5
Citrus aurantifolia	Mexican lime	MC	108	22	3,273,200	1,479	100.0
Citrus micrantha	Micrantha	MC	108	22	7,656,308	3,481	99.7
Citrus reticulata	Mangshan mandarinc	MN	121	4	3,290,081	1,541	99.7
Citrus clementina	Clementine mandarin	MA	142	38	8,355,334	3,702	100.0
Citrus deliciosa	Willowleaf mandarin	MA	142	38	3,372,519	1,466	100.0
Citrus reticulata	Ponkan mandarin	MA	142	38	1,797,993	817	100.0
Citrus unshiu	Satsuma mandarin	MA	142	38	1,693,894	765	100.0
Citrus tangerina	Dancy mandarin	MA	142	38	3,903,551	1,779	100.0
Citrus nobilis	King mandarin	MA	142	38	1,651,462	750	100.0
Citrus reticulata	W. Murcott mandarin	MA	142	38	2,317,975	1,074	100.0
Citrus reticulata	Huanglingmiao mandarinc	MA	142	38	4,199,260	1,966	99.7
Citrus limonia	Rangpur lime	MA	148	40	3,847,026	1,733	100.0
Citrus reshni	Cleopatra mandarin	MA	149	40	8,333,902	3,592	100.0
Citrus sunki	Sunki mandarin	MA	149	40	1,093,257	494	100.0
Citrus ichangesis	Ichang papeda	PA	168	6	4,379,125	1,981	99.8
Citrus madurensis	Calamondin	FO	178	39	994,327	443	99.8
Fortunella margarita	Nagami Kumquat	FO	183	39	999,497	439	99.9
Poncirus trifoliata	Pomeroy	PO	216	44	12,053,896	5,359	100.0
Citrus medica	Buddhás Hand citron	CI	216	61	2,608,145	1,172	100.0
Citrus medica	Mac Veu mountain Citron	CI	216	61	3,918,552	1,766	100.0
Citrus medica	Humpang citron	CI	216	61	2,334,979	1,054	100.0
Citrus medica	Corsican citron	CI	216	61	2,096,451	955	100.0
Microcitrus australasica	Australian finger lime	MI	260	71	2,225,093	1,003	100.0
Microcitrus australis	Australian round lime	MI	293	78	1,698,579	763	99.9
Eremocitrus glauca	Australian desert lime	ER	362	78	1,385,587	622	100.0
Severinia buxifolia	Chinese box orange	SB	430	136	6,346,507	2,926	99.9

Note.—Identity of chloroplast genomes was deduced from the presence of SNVs and indels. The genome sequence of the Citrus sinensis chloroplast was used as the genome of reference (Bausher et al. 2006). After variant calling, SNVs and indels were manually curated. Sequencing statistics (number of mapped read, mean coverage, genome fraction with coverage over 15×) determined after excluding and inverted repeat regions and sequences homologous to nuclear DNA. Chloroplast types: PU, pummelo; MC, Micrantha; MN, mangshan; MA, mandarin; PA, papeda; FO, Fortunella; PO, Poncirus; CI, citron; MI, Microcitrus; ER, Eremocitrus; SB, Severinia.

^aThere were two nonconcordant positions (41051 and 78452) between the Sanger reference sequence of the C. sinensis chloroplast and the C. sinensis chloroplast genome resequenced here. The nucleotide at position 41051 in the reference sequence was not confirmed in any of the 34 genomes analyzed, whereas that at position 78452 was observed solely in the 11 mandarins clustered in group MA.

^bSimilarly, indels at positions 46206, 49034, 78458, and 83617 absent in the reference genome were observed in all 34 genomes resequenced in this work. These discrepancies that may be attributed to Sanger sequencing errors in the reference genome were not used in further comparative analyses.

^cThose genomes were reanalyzed from original published sweet orange genome sequences (Xu et al. 2013).