Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and Chloroplast DNA Extraction
2.2. Annotation and Physical Map Drawing
2.3. SSR and Repeat Sequences Analysis
2.4. Genomic Comparative Analysis
2.5. Phylogenesis Analysis
3. Results
3.1. CPG Organizations
3.2. Analysis of the Repeat and the SSRs
3.3. Comparative Genomics
3.4. Phylogenetic Analysis
3.5. Plant Morphology
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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Lable | Species | Genome Size (bp) | LSC Region (bp) | IR Region (bp) | SSC Region (bp) | Number of Genes | PCGs | tRNAs | rRNAs | GC Content (%) | Number of Accession in Genbank |
---|---|---|---|---|---|---|---|---|---|---|---|
OB | H. officinalis var. biloba | 160,011 | 88,136 | 26,568 | 18,739 | 132 | 87 | 37 | 8 | 39.22 | OM912810 |
R | H. rostrata | 160,070 | 88,194 | 26,558 | 18,760 | 120 | 76 | 36 | 8 | 39.26 | MW800876 |
OO | H. officinalis | 160,153 | 88,234 | 26,569 | 18,781 | 131 | 86 | 37 | 8 | 39.26 | OM912809 |
Category | Gene Group | Gene Name |
---|---|---|
Photosynthesis | Photosystem I | psaA, psaB, psaC, psaI, psaJ |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
NADH dehydrogenase | ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK, ndhA*, ndhB(2), ndhA*, ndhB(2) | |
Cytochrome b/f complex | petA, petD, petG, petL, petN, petB*, petB* | |
ATP synthase | atpA, atpB, atpE, atpH, atpI, atpF*, atpF* | |
Large subunit of rubisco | rbcL | |
Self-replication | Proteins ribosomal (LSU) | rpl14, rpl16, rpl20, rpl23(2), rpl32, rpl33, rpl36, rpl2*(2), rpl2*(2), rpl32 |
Proteins ribosomal (SSU) | rps11, rps12**(2), rps14, rps15, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8, rps16*, rps16* | |
RNA polymerase | rpoA, rpoB, rpoC2, rpoC1*, rpoC1* | |
Ribosomal RNAs | rrn16(2), rrn23(2), rrn4.5(2), rrn5(2) | |
Transfer RNAs | tRNA-Leu, 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, trnL-UAA*, trnL-UAG, trnM-CAU, trnN-GUU, 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, trnA*, trnI, trnI*, trnI-CAU, trnI-GAU*, trnL, trnL*trnM, trnV, trnV-GAC, trnA-UGC*, trnD, trnA-UGC*(2), trnI-CAU(2), trnI-GAU*(2), trnL, trnL-UAA*, trnN-GUU(2), trnV-GAC(2), trnfM-CAU | |
Other genes | Maturase | matK |
Protease | clpP** clpP** | |
Envelope membrane | cemA | |
Acetyl-CoA carboxylase | accD | |
c-type cytochrome synthesis gene | ccsA | |
Translation initiation factor | infA | |
Conserved hypothetical chloroplast ORF | ycf1, ycf15(2), ycf2(2), ycf4, ycf3**, ycf3** |
Gene | OO | OB | R | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EpI | InI | EpII | InII | EpIII | EpI | InI | EpII | InII | EpIII | EpI | InI | EpII | InII | EpIII | |
rps12 a | 114 | 536 | 232 | 26 | 114 | 536 | 232 | 26 | 114 | 536 | 232 | 26 | |||
trnK-UUU | 37 | 2491 | 35 | 37 | 2491 | 35 | 37 | 2491 | 35 | ||||||
rps16 | 42 | 824 | 219 | 42 | 824 | 219 | |||||||||
trnG-UCC | 24 | 770 | 48 | 24 | 768 | 748 | 24 | 766 | 48 | ||||||
atpF | 144 | 711 | 411 | 144 | 709 | 411 | |||||||||
rpoC1 | 434 | 722 | 1624 | 434 | 722 | 1624 | |||||||||
ycf3 | 126 | 734 | 228 | 728 | 153 | 126 | 734 | 228 | 728 | 153 | |||||
trnL | 35 | 491 | 50 | ||||||||||||
trnL-UAA | 35 | 491 | 50 | 35 | 491 | 50 | |||||||||
trnV-UAC | 39 | 584 | 37 | 39 | 584 | 37 | 39 | 584 | 37 | ||||||
rps12 b | 114 | 536 | 232 | 26 | 114 | 536 | 232 | 26 | 114 | 536 | 232 | 26 | |||
clpP | 69 | 785 | 291 | 628 | 246 | 69 | 782 | 291 | 629 | 246 | |||||
petB | 6 | 784 | 642 | 6 | 779 | 642 | |||||||||
rpl2 a | 393 | 658 | 432 | 393 | 658 | 432 | |||||||||
ndhB a | 777 | 700 | 756 | 777 | 700 | 756 | |||||||||
trnI-GAU a | 42 | 936 | 35 | 42 | 936 | 35 | 42 | 936 | 35 | ||||||
trnA-UGC a | 38 | 799 | 35 | 38 | 799 | 35 | 38 | 799 | 35 | ||||||
ndhA | 552 | 1080 | 540 | 552 | 1078 | 540 | |||||||||
trnA | 38 | 799 | 35 | ||||||||||||
trnI | 42 | 936 | 35 | ||||||||||||
trnA-UGC b | 38 | 799 | 35 | 38 | 799 | 35 | |||||||||
trnI-GAU b | 42 | 936 | 35 | 42 | 936 | 35 | |||||||||
ndhB b | 777 | 700 | 756 | 777 | 700 | 756 | |||||||||
rpl2 b | 393 | 658 | 432 | 393 | 658 | 432 |
Botanical Traits | OO | OB | R |
---|---|---|---|
Leaf | White, long hair, concave leaf apex, shallow lobes in two obtuse circles. | White, long hair, short, acute or obtuse at the apex of leaves, without notch. | White, reddish-brown hair, apex broadly rounded, with a short, acute point. |
Fruit | Aggregate fruit; oblong ovoid | Aggregate fruit; oblong ovoid. | Aggregate fruit is cylindrical and upright. |
Flower | White, fragrant, 12 cm in diameter. | White, fragrant, 13 cm in diameter. | White, fragrant, 9 cm in diameter. |
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Xu, Q.; Li, Z.; Wu, N.; Yang, J.; Yuan, L.; Zhao, T.; Sima, Y.; Xu, T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes 2023, 14, 1262. https://doi.org/10.3390/genes14061262
Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes. 2023; 14(6):1262. https://doi.org/10.3390/genes14061262
Chicago/Turabian StyleXu, Qinbin, Zhuoran Li, Nannan Wu, Jing Yang, Lang Yuan, Tongxing Zhao, Yongkang Sima, and Tao Xu. 2023. "Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants" Genes 14, no. 6: 1262. https://doi.org/10.3390/genes14061262
APA StyleXu, Q., Li, Z., Wu, N., Yang, J., Yuan, L., Zhao, T., Sima, Y., & Xu, T. (2023). Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes, 14(6), 1262. https://doi.org/10.3390/genes14061262