Table 1.
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).