Figures (10)  Tables (3)
    • Figure 1. 

      Carya illinoinensis cv. Xinxuan-4. (a) Male flower. (b) Female flower. (c) Fruits on the tree. (d) Fruit without husk, scale bar = 2 cm.

    • Figure 2. 

      Circular representation of the cp genome of C. illinoinensis cv. Xinxuan-4.

    • Figure 3. 

      GC content of the C. illinoinensis cv. Xinxuan-4 cp genome.

    • Figure 4. 

      Codon usage frequency of the C. illinoinensis cv. Xinxuan-4 cp genome.

    • Figure 5. 

      Size and type of the long repeats located in the C. illinoinensis cv. Xinxuan-4 cp genome.

    • Figure 6. 

      SSRs distribution in the cp genomes of the C. illinoinensis cv. Xinxuan-4. (a) Type and number of SSRs. (b) Type and number of SSR repeats. (c) Number of SSRs in various location. (d) Number of SSRs in three locations.

    • Figure 7. 

      Comparing the LSC, SSC, and IR locations of five selected cp genomes in the Carya.

    • Figure 8. 

      Sequence identity plot comparing the cp genomes among Carya with C. illinoinensis cv. Xinxuan-4 set as a reference.

    • Figure 9. 

      Sliding window analysis of the cp genome for nucleotide diversity (pi) of three species in Carya.

    • Figure 10. 

      Phylogenetic tree of 18 related species based on the whole cp genome.

    • SpeciesXinxuan-4Pawnee87MX3-2.11LakotaWichitaCathayensis
      Genome size (bp)160,819160,819160,545160,819160,532160,825
      LSC size (bp)90,02290,02289,93390,04189,79990,115
      SSC size (bp)18,79118,79118,57618,79018,75118,760
      IR size (bp)26,00326,00326,01825,99425,99125,975
      Total genes132131124123128129
      Protein-coding genes87(8)86(7)84(6)83(6)83(6)84
      tRNAs37(7)37(8)32(6)32(6)37(8)37(7)
      rRNAs8(4)8(4)8(4)8(4)8(4)8(4)
      GC content (%)36.136.136.236.136.236.1

      Table 1. 

      Features of the cp genomes of C. illinoinensis cv. Xinxuan-4 and five related materials.

    • CategoryGene group
      PhotosynthesisSubunits of photosystem IpsaA, psaB, psaC, psaI, psaJ
      Subunits of photosystem IIpsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
      Subunits of NADHndhAb, ndhBab, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
      Cytochrome b/f complexpetA, petBb, petDb, petG, petL, petN
      Subunits of ATP synthaseatpA, atpB, atpE, atpFb, atpH, atpI
      Large subunit of rubiscorbcL
      Self-replicationLarge ribosomal subunitrpl14, rpl16b, rpl2ac, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl36
      Small ribosomal subunitrps11, rps12ab, rps14, rps15, rps16b, rps18, rps19, rps2, rps3, rps4, rps7a, rps8
      Subunits of RNA polymeraserpoA, rpoB, rpoC1b , rpoC2
      Ribosomal RNAsrrn16a, rrn23a, rrn4.5a, rrn5a
      Transfer RNAs
      trnA-UGCab, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCCb, trnG-UCC, trnH-GUG, trnI-CAUa, trnI-GAUab, trnK-UUUb, trnL-CAAa, trnL-UAAb, trnL-UAG, trnM-CAU, trnN-GUUa, trnP-UGG, trnQ-UUG, trnR-ACGa, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GACa, trnV-UACb, trnW-CCA, trnY-GUA, trnfM-CAU
      Other genesMaturasematK
      ProteaseclpPc
      Envelope membrane proteincemA
      Acetyl-CoA carboxylaseaccD
      c-type cytochrome synthesis geneccsA
      Unknown function genesConserved open reading framesycf1a, ycf15a, ycf2a, ycf3c, ycf4
      a Gene with two copies, b Gene with one intron, c Gene with two introns.

      Table 2. 

      Annotated genes in the cp genome of C. illinoinensis cv. Xinxuan-4.

    • Gene groupDifferent geneXinxuan4Pawnee87MX3-2.11LakotaCathayensis
      Protein-coding genesrps1222102
      rps1611001
      psbZ11110
      lhbA00001
      ycf1522220
      tRNA genestrnA-UGC22220
      trnG-UCC10000
      trnI-GAU22000
      trnL-UAA11001
      trnV-UAC11001
      rna-UGC00002

      Table 3. 

      Different genes and gene copies in the cp genomes among five Carya materials.