Figures (6)  Tables (4)

    • Figure 1. 

      Chloroplast genome map of C. meiocarpa and C. oleifera.

    • Figure 2. 

      Comparison of repetitive sequences in C. meiocarpa and C. oleifera. (a) Number of scattered repetitive by length in different regions. (b) The number and distribution of Simple Sequence Repeats (SSR)s. (c) Frequency of SSRs in A and T.

    • Figure 3. 

      Comparison of the Large single copy (LSC), Inverted repeat (IR), Small single copy (SSC) junction positions among 11 tea-oil Camellia species.

    • Figure 4. 

      Identity plots comparing the chloroplast genomes of 11 Camellia accessions. The vertical scale indicates the percentage of identity, ranging from 50 to 100%. The horizontal axis indicates the coordinates within the chloroplast genome. Genome regions are color coded, including protein-coding, rRNA, tRNA, intron, and conserved non-coding sequences (CNS).

    • Figure 5. 

      The nuclear divergence in C. meiocarpa and C. oleifera chloroplast genomes by (a) sliding window analysis of the whole genomes; (b) gene regions.

    • Figure 6. 

      Phylogenetic tree reconstruction of 27 Camellia species based on (a) protein-coding genes and (b) whole chloroplast genome sequences by the Bayesian method.

    • Genome featureCKXXGHZP
      Genome size (bp)156,549156,512157,009
      LSC length (bp)86,26386,22486,637
      SSC length (bp)18,40018,40218,290
      IR length (bp)25,94325,94326,041
      Number of genes133133133
      Number of protien-coding genes878787
      Number of pseudo222
      Number of tRNA genes373737
      Number of rRNA genes888
      GC content in LSC (%)35.3335.3435.30
      GC content in SSC (%)30.5830.5730.52
      GC content in IR (%)43.0343.0342.99
      Total GC content (%)37.3237.3337.29
      GenBank numberMZ151356MZ151355MZ151357

      Table 1. 

      Features of C. meiocarpa and C. oleifera chloroplast genomes.

    • ZHPXGCKX
      Total number494949
      Forward151617
      Palindrome222020
      Reverse999
      Complementary343
      Gene NtrnS-GCU, trnG-GCC, trnS-UGA, trnfM-CAU,
      ndhC, trnV-UACa, petD, ycf2, ndhA, ycf1,
      rpoC2b, rpoBc, trnA-UGCd
      SSR Loci (N)524849
      P1 Loci (N)514749
      Pc Loci (N)110
      LSC403536
      IRA222
      SSC899
      IRB222
      a: special in ZHP; b, c: special in XG; d: special in CKX.

      Table 2. 

      Features of repetitive sequences in C. meiocarpa and C. oleifera.

    • Indel (bp)123456910−2021−Total
      Number (N)28125210516372
      Proportion (%)38.8916.676.942.781.396.941.398.334.17
      SNP typeG/AC/TA/CG/TC/GT/A
      Number (N)36322727511138
      Proportion (%)26.0923.1919.5719.573.627.97

      Table 3. 

      Indel and SNP types among three chloroplast genomes.

    • PrimersLociSNPIndel
      ZDJ01TCCACTATTT[C/A]AATTATAAAA10
      ZDJ01CAACCCATAA[C/-]CCATAAAAAT01
      ZDJ03CCCAAAAAAT[G/A]GATTTTGGTT10
      ZDJ15TCAATGGCCC[T/C]CCTACGTAGT10
      ZDJ45TCCCATATAT[T/-]AAATATTAAA01
      ZDJ51ATTGAAAGCT[A/G]GGATTTCTAG10
      ZDJ54AATCCTTGTT[T/G]CGGAGTCGAT10
      ZDJ55ACCAAAAAAT[A/C]TTTTTTGCTT10
      ZDJ59TTCATCTATT[T/C]CATGACCGGA10
      ZDJ60GACCAAGAAG[G/-]ATTCTCTTTC01
      ZDJ69ATAAAAAATT[A/T]CCCCCTGCAA10
      ZDJ72AAAATCATGT[G/A]TTGGTCCAGA10
      ZDJ76TTCAAAATGG[C/-]TTTCAAATTA01
      ZDJ76AAAGAATAGT[A/C]AATTTTTGCA10
      ZDJ76AGAATAATTT[G/T]AATCTTAAAA10
      ZDJ77GTATAACCCC[C/T]TTTTGCTTTC10
      ZDJ80TAAGAATGGG[G/T]GACGGTATTC10
      ZDJ83GAATTCTGTG[A/G]AAAGCCGTAT10
      ZDJ84AAGAGAATCC[T/-]TCTTGGTCGT01
      ZDJ85TCCGGTCATG[A/G]AATAGATGAA10
      In Loci, the variant in left side was C. oleifera and the right side was C. meiocarpa.

      Table 4. 

      The SNP and Indel in the targeted regions.