Figures (6)  Tables (1)

    • Figure 1. 

      Annotation map of the Aquilaria plastome. Genes listed inside and outside the circle are transcribed clockwise and counterclockwise, respectively, with genes color-coded based on functional classification.

    • Figure 2. 

      Comparison of the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) region borders of Aquilaria plastomes. The LSC, IR, and SSC regions are depicted with blue, orange, and green blocks, respectively. Gene boxes above the block are transcribed counterclockwise while those below the block are transcribed clockwise. (Representative plastomes from Supplemental Fig. S2).

    • Figure 3. 

      Comparison of nucleotide variability values among 37 plastomes using window sliding analysis. The x-axis indicates the position of the midpoint of the window, while the y-axis indicates the nucleotide diversity of each window.

    • Figure 4. 

      (a) Distribution of different types of large sequences repeat (LSRs) in Aquilaria plastomes, including complementary (C), forward (F), palindromic (P), and reverse (R) type repeats. (b) Distribution of distinct types of simple sequence repeats (SSRs) in Aquilaria plastomes.

    • Figure 5. 

      Values of synonymous (Ks) and non-synonymous (Ka) substitution rates for 79 protein-coding genes in Aquilaria.

    • Figure 6. 

      Phylogenetic tree depicting relationships among Aquilaria species. Red circles indicates bootstrap support (BS) values greater than 80% and posterior probability (PP) values exceeding 1. Yellow circles indicates BS values ranging from 40% to 80%, and PP values ranging from 0.7 to 0.9. Grey circles indicates BS values below 40% and PP values less than 0.7.

    • Category Group of genes Names of genes
      Photosynthesis Subunits of photosystem I psaA, psaB, psaC(2), psaI, psaJ
      Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
      Subunits of NADH dehydrogenase ndhA*(2), ndhB*(2), ndhC, ndhD(2), ndhE(2), ndhF, ndhG(2), ndhH(2), ndhI(2), ndhJ, ndhK
      Subunits of cytochrome b/f complex petA, petB*, petD*, petG, petL, petN
      Subunits of ATP synthase atpA, atpB, atpE, atpF*, atpH, atpI
      Large subunit of rubisco rbcL
      Subunits photochlorophyllide reductase −
      Self-replication Proteins of large ribosomal subunit rpl14, rpl16, rpl2*(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36
      Proteins of small ribosomal subunit rps11, rps12**(2), rps14, rps15(2), rps16*, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8
      Subunits of RNA polymerase rpoA, rpoB, rpoC1*, rpoC2
      Ribosomal RNAs rrn16(2), rrn23(2), rrn4.5(2), rrn5(2)
      Transfer RNAs trnA-UGC*(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC*, trnH-GUG, trnI-CAU(2), trnI-GAU*(2), trnK-UUU*, trnL-CAA(2), trnL-UAA*, trnL-UAG(2), trnM-CAU, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC*,
      trnW-CCA, trnY-GUA, trnfM-CAU
      Other genes Maturase matK
      Protease clpP
      Envelope membrane protein cemA
      Acetyl-CoA carboxylase accD
      c-type cytochrome synthesis gene ccsA
      Translation initiation factor −
      other −
      Genes of unknown function Conserved hypothetical chloroplast ORF ycf1(2), ycf15(2), ycf2(2), ycf3**, ycf4
      Gene*: Gene with one intron; Gene**: Gene with two introns; Gene(2): Number of copies of multi-copy genes.

      Table 1. 

      Genes present within Aquilaria plastomes.