Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Extraction of cpDNA, and Sequencing
2.2. CpDNA Assembly and Annotation
2.3. Analysis of the Cp Genome for Repetitive Sequences
2.4. Codon Preference Analysis
2.5. Sequence Variation Analysis
2.6. Phylogenetic Relationship Analysis
3. Results
3.1. Chloroplast Genomic Structure of A. chinensis ’Hongyang’
3.2. Chloroplast Genome Composition of Actinidia
3.3. Codon Usage in the Chloroplast Genome of A. chinensis ’Hongyang’
3.4. Detection of Repeated Sequences and SSRs in A. chinensis ‘Hongyang’ cpDNA
3.5. Comparative Analysis of Fifteen Species Chloroplast Genomic Structure
3.6. Phylogenetic Analysis of 29 Taxa of the Actinidiaceae Based on cpDNA Sequences
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Region | A (%) | C (%) | G (%) | T (U) (%) | AT (%) | GC (%) |
---|---|---|---|---|---|---|
LSC | 31.53 | 18.16 | 17.34 | 32.97 | 64.50 | 35.50 |
SSC | 33.83 | 16.67 | 14.48 | 35.02 | 68.85 | 31.15 |
IRs | 28.78 | 20.57 | 22.31 | 28.33 | 57.11 | 42.89 |
Total | 30.92 | 18.98 | 18.23 | 31.88 | 62.80 | 37.20 |
Species | GenBank Number | Genome Size (bp) | LSC (bp) | SSC (bp) | IR (bp) | Genes | PCGs | tRNAs | rRNAs | GC Content (%) |
---|---|---|---|---|---|---|---|---|---|---|
A. chinensis | 156,216 | 88,316 | 20,332 | 23,784 | 132 | 86 | 38 | 8 | 37.20 | |
A. arguta | 157,611 | 88,532 | 20,463 | 24,308 | 133 | 84 | 41 | 8 | 37.10 | |
A. deliciosa | 156,741 | 88,267 | 20,332 | 24,071 | 130 | 83 | 39 | 8 | 37.20 | |
A. eriantha | 156,964 | 88,639 | 20,541 | 23,892 | 131 | 84 | 39 | 8 | 37.20 | |
A. chinensis ‘HFY01’ | 156,322 | 88,085 | 20,331 | 23,953 | 131 | 84 | 39 | 8 | 37.20 | |
A. chinensis ’Jinguo’ | 156,743 | 88,265 | 20,332 | 24,073 | 132 | 85 | 39 | 8 | 37.20 | |
A. kolomikta | 157,425 | 88,498 | 20,475 | 24,226 | 131 | 84 | 39 | 8 | 37.20 | |
A. latifolia | 156,873 | 88,666 | 21,453 | 23,377 | 132 | 83 | 41 | 8 | 37.20 | |
A. macrosperma | 156,231 | 88,214 | 20,577 | 23,720 | 132 | 85 | 39 | 8 | 37.20 | |
A. melanandra | 156,124 | 88,006 | 20,332 | 23,893 | 131 | 84 | 39 | 8 | 37.20 | |
A. polygama | 156,583 | 88,568 | 20,397 | 23,809 | 131 | 83 | 40 | 8 | 37.20 | |
A. rufa | 156,543 | 88,436 | 20,307 | 23,900 | 131 | 84 | 39 | 8 | 37.20 | |
A. valvata | 156,660 | 88,397 | 20,447 | 23,908 | 134 | 85 | 41 | 8 | 37.20 | |
A. zhejiangensis | 156,717 | 86,483 | 22,574 | 23,840 | 128 | 81 | 39 | 8 | 37.20 | |
A. chinensis ‘Hongyang’ | 156,267 | 87,866 | 20,335 | 24,033 | 132 | 85 | 39 | 8 | 37.20 |
Category | Gene Group | Gene Name | Number |
---|---|---|---|
Photosynthesis | Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ | 5 |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 | |
Subunits of NADH dehydrogenase | ndhA *, ndhB *(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 | |
Subunits of the cytochrome b/f complex | petA, petB *, petD *, petG, petL, petN | 6 | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF *, atpH, atpI | 6 | |
Large subunit of rubisco | rbcL | 1 | |
Self-replication | Proteins of large ribosomal subunits | rpl14, rpl16 *, rpl2 *, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 | 9 |
Proteins of the small ribosomal subunit | rps11, rps12 **(2), rps14, rps15, rps16 *, rps18, rps19, rps2, rps3, rps4, rps7 (2), rps8 | 14 | |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1 *, rpoC2 | 4 | |
Ribosomal RNAs | rrn16 (2), rrn23 (2), rrn4.5 (2), rrn5 (2) | 8 | |
Transfer RNAs | trnA(UGC) *(2), trnC(GCA), trnD(GUC), trnE(UUC), trnF(GAA), trnG(GCC), trnG(UCC) *, trnH(GUG) (2), trnI(CAU) (2), trnI(GAU) *(2), trnK(UUU) *, trnL(CAA) (2), trnL(UAA) *, trnL(UAG), 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) (2) | 39 | |
Other genes | Maturase | matK | 1 |
Envelope membrane protein | cemA | 1 | |
Acetyl-CoA carboxylase | accD | 1 | |
c-type cytochrome synthesis gene | ccsA | 1 | |
Translation initiation factor | infA | 1 | |
Genes of unknown function | Conserved hypothetical cp open reading framework | ycf1 (2), ycf15 (2), ycf2 (2), ycf3 **, ycf4 | 8 |
Total | 132 |
Genes | Local | Exon1 | Intron1 | Exon2 | Intron2 | Exon3 |
---|---|---|---|---|---|---|
rps12 | IRa + LSC | 114 | 536 | 232 | 26 | |
trnK(UUU) | LSC | 37 | 2489 | 39 | ||
rps16 | LSC | 38 | 875 | 226 | ||
trnG(UCC) | LSC | 23 | 689 | 48 | ||
atpF | LSC | 145 | 733 | 410 | ||
rpoC1 | LSC | 453 | 748 | 1605 | ||
ycf3 | LSC | 126 | 710 | 228 | 743 | 153 |
trnL(UAA) | LSC | 37 | 504 | 50 | ||
trnV(UAC) | LSC | 39 | 595 | 37 | ||
rps12-2 | IRb + LSC | 114 | 536 | 232 | 26 | |
petB | LSC | 6 | 753 | 645 | ||
petD | LSC | 8 | 777 | 475 | ||
rpl16 | LSC | 9 | 1055 | 399 | ||
rpl2 | LSC | 405 | 664 | 441 | ||
ndhB | IRa | 777 | 679 | 756 | ||
trnI(GAU) | IRa | 42 | 942 | 35 | ||
trnA(UGC) | IRa | 38 | 798 | 35 | ||
ndhA | SSC | 553 | 1085 | 539 | ||
trnI(GAU)-2 | IRb | 42 | 942 | 35 | ||
ndhB-2 | IRb | 777 | 679 | 756 | ||
trnA(UGC)-2 | IRb | 38 | 798 | 35 |
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Liu, H.; Liu, X.; Sun, C.; Li, H.-L.; Li, Z.-X.; Guo, Y.; Fu, X.-Q.; Liao, Q.-H.; Zhang, W.-L.; Liu, Y.-Q. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’. Genes 2023, 14, 2136. https://doi.org/10.3390/genes14122136
Liu H, Liu X, Sun C, Li H-L, Li Z-X, Guo Y, Fu X-Q, Liao Q-H, Zhang W-L, Liu Y-Q. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’. Genes. 2023; 14(12):2136. https://doi.org/10.3390/genes14122136
Chicago/Turabian StyleLiu, Han, Xia Liu, Chong Sun, Hong-Lei Li, Zhe-Xin Li, Yuan Guo, Xue-Qian Fu, Qin-Hong Liao, Wen-Lin Zhang, and Yi-Qing Liu. 2023. "Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’" Genes 14, no. 12: 2136. https://doi.org/10.3390/genes14122136
APA StyleLiu, H., Liu, X., Sun, C., Li, H.-L., Li, Z.-X., Guo, Y., Fu, X.-Q., Liao, Q.-H., Zhang, W.-L., & Liu, Y.-Q. (2023). Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’. Genes, 14(12), 2136. https://doi.org/10.3390/genes14122136