The complete plastid genome of Citrus hystrix DC. 1813 (Rutaceae) and its phylogenetic analysis

Abstract

The complete plastome size of Citrus hystrix DC. 1813 was 159,893 bp in length and has a typical quadripartite structure. The 87,148-bp-long large single-copy and the 18,763-bp-long small single-copy regions were separated by a pair of inverted repeats (each 26,991 bp). The plastome was predicted to contain 132 genes, of which 87 were CDS, 37 were tRNA, and eight were rRNA genes. The plastome was A/T biassed, and the overall GC content was 38.4%. Using maximum likelihood and Bayesian inference methods, the phylogenetic analysis of the complete plastome sequence revealed a close relationship between C. hystrix and C. aurantiifolia, placing them under the same clade as C. micrantha.

Keywords: Aurantidioideae; Citrus micrantha; genetic resources; kaffir lime; limau purut.

Figure 1.

Morphological characteristics of Citrus hystrix. (A) distinctive double leaves, (B) small, fragrant, white flower, and (C) large, verrucose, bumpy fruit. Photos by S.Y. Lee.

Figure 2.

Plastid genome map of Citrus hystrix. Genes on inside of map are transcribed in clockwise direction; genes on outside of map are transcribed in counter clockwise direction.

Figure 3.

Phylogenetic tree based on the plastid genome sequence of 31 selected species of Citrus, with Ruta chalepensis (GenBank accession number: ON641291; unpublished); Zanthoxylum pinnatum (GenBank accession number: MN968553; Reichelt et al. 2021) included as outgroup. For the maximum likelihood, the GTR+G substitution model was employed, and branch supports were calculated under 1,000 bootstrap replicates; for the Bayesian inference, a 4-by-4 nucleotide model was applied, and MCMC was performed under 2,000,000 generations with sampling taken at every 100 cycles. The bootstrap support (BS; left) and posterior probability (PP; right) values are indicated at each branch node, of which BS ≥ 75% and PP ≥ 0.95 are indicated with an asterisk (*). The following sequences were used: C. aurantiifolia (GenBank accession number: KJ865401; Su et al. 2014), C. aurantium (GenBank accession number: MZ147612; unpublished), C. australasica (GenBank accession number: MZ929414; Cai et al. 2022), C. cavaleriei (GenBank accession number: MT880606; Zhang et al. 2020a), C. depressa (GenBank accession number: LC147381; Ishikawa et al. 2016), C. erythrosa (GenBank accession number: MW722946; Shin et al. 2022), C. hindsii (GenBank accession number: MN073195; Xu et al. 2019), C. hystrix (GenBank accession number: PQ149287; this study), C. hongheensis (GenBank accession number: MT880607; Zhang et al. 2020b), C. indica (GeneBank accession number: ON872191; Shi et al. 2023), C. jambhiri (GenBank accession number: ON872192; Shi et al. 2023), C. japonica (GenBank accession number: MN495932), C. junos (GenBank accession number: ON065547; Shi et al. 2023), C. keraji (GenBank accession number: ON065548; Shi et al. 2023), C. latipes (GenBank accession number: LC794892), C. limonia (GenBank accession number: ON872193; Shi et al. 2023), C. madurensis (GenBank accession number: ON065549; Shi et al. 2023), C. mangshanensis (GenBank accession number: ON065550; Shi et al. 2023), C. maxima (GenBank accession number: KY055833; Liu and Shi 2017), C. medica (GenBank accession number: MT106673; Zhang and Bai 2020), C. micrantha (GenBank accession number: ON597621; Madayag et al. 2022), C. nobilis (GenBank accession number: ON872195; Shi et al. 2023), C. oto (GenBank accession number: ON065551; Shi et al. 2023), C. platymamma (GenBank accession number: KR259987; Lee et al. 2015), C. polytrifolia (GenBank accession number: MK250977; Li et al. 2019), C. reticulata (GenBank accession number: KY596676; unpublished), C. sinensis (GenBank accession number: DQ864733; Bausher et al. 2006), C. tachibana (GenBank accession number: ON065552; Shi et al. 2023), C. tangerina (GenBank accession number: ON872196; Shi et al. 2023), C. tarogayo (GenBank accession number: ON065548; Shi et al. 2023), and C. trifoliata (GenBank accession number: MN102360; He et al. 2020).