Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae
Abstract
1. Introduction
2. Results and Discussion
2.1. Chloroplast Genome of Paphiopedilum delenatii
2.2. Repeat and Microsatellite Analysis
2.3. Phylogenetic and Species Resolution Analyses
2.4. Divergence of Hotspot Regions
3. Materials and Methods
3.1. Plant Material, DNA Extraction, and Sequencing
3.2. Read Data Processing and Chloroplast Genome Assembly
3.3. Repeat Sequence and Microsatellite Identification
3.4. Examination of IR Junctions
3.5. Phylogenetic Analysis
3.6. Nucleotide Variability Calculation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviation
IUCN | International Union for Conservation of Nature |
Cp | chloroplast |
CR | Critically endangered |
IR | Inverted repeat region |
SSC | Small single-copy region |
LSC | Large single-copy region |
gBGC | GC-biased gene conversion |
SSR | Simple sequence repeat |
SNP | Single nucleotide polymorphism |
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Classification of Genes | Name of Genes | Number | |
---|---|---|---|
RNA genes | Ribosomal RNAs | rrn4.5(× 2), rrn5(× 2), rrn16(× 2), rrn23(× 2) | 8 |
Transfer RNAs | trnA_UGC(× 2), trnC_GCA, trnD_GUC, trnE_UUC, trnF_GAA, trnfM_CAU, trnG_GCC, trnG_UCC, trnH_GUG(× 2), 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 | 39 | |
Protein-coding genes | Photosystem I | psaA, psaB, psaC, psaI, psaJ | 5 |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 | |
Cytochrome | petA, petB, petD, petG, petL, petN | 6 | |
ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | 6 | |
Rubisco | rbcL | 1 | |
Ribosomal proteins-small units | rps11, rps12(× 2), rps14, rps15(× 2), rps16, rps18, rps19(× 2), rps2, rps3, rps4, rps7(× 2), rps8 | 16 | |
Ribosomal proteins-large units | rpl14, rpl16, rpl2(× 2), rpl20, rpl22, rpl23(× 2), rpl32(× 2), rpl33, rpl36 | 12 | |
RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | 4 | |
Miscellaneous | accD, ccsA, cemA, clpP, infA, matK | 6 | |
Hypothetical chloroplast reading frames (ycf) | ycf1(× 2), ycf2(× 2), ycf3, ycf4 | 6 | |
Pseudogenes | NADH dehydrogenase | ndhB(× 2), ndhC, ndhD, ndhJ, ndhK | 6 |
Total | 130 |
Species | Paphiopedilum delenatii | Paphiopedilumarmeniacum | Paphiopedilumniveum | Paphiopedilumdianthum |
---|---|---|---|---|
Total length (bp) | 160,955 | 162,682 | 159,108 | 154,699 |
IR length (bp) | 34,196 | 33,641 | 31,978 | 32,711 |
LSC length (bp) | 89,869 | 91,734 | 89,958 | 86,861 |
SSC length (bp) | 2694 | 3666 | 5194 | 2416 |
Total gene number | 130 | 129 | 126 | 130 |
Coding sequence (CDS) number | 77 | 77 | 74 | 79 |
rRNA number | 8 | 8 | 8 | 8 |
tRNA number | 39 | 38 | 38 | 38 |
Pseudogene number | 6 | 6 | 6 | 5 |
Overall GC content (%) | 35.6 | 35.4 | 35.0 | 35.0 |
GC content of IR (%) | 39.3 | 39.0 | 40.0 | 39.0 |
GC content of LSC (%) | 33 | 32.6 | 32.0 | 33.0 |
GC content of SSC (%) | 28.5 | 31.0 | 29.0 | 29.0 |
GenBank accession | MK463585 | NC_026779.1 | NC_026776.1 | NC_036958.1 |
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Vu, H.-T.; Tran, N.; Nguyen, T.-D.; Vu, Q.-L.; Bui, M.-H.; Le, M.-T.; Le, L. Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae. Plants 2020, 9, 61. https://doi.org/10.3390/plants9010061
Vu H-T, Tran N, Nguyen T-D, Vu Q-L, Bui M-H, Le M-T, Le L. Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae. Plants. 2020; 9(1):61. https://doi.org/10.3390/plants9010061
Chicago/Turabian StyleVu, Huyen-Trang, Ngan Tran, Thanh-Diem Nguyen, Quoc-Luan Vu, My-Huyen Bui, Minh-Tri Le, and Ly Le. 2020. "Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae" Plants 9, no. 1: 61. https://doi.org/10.3390/plants9010061
APA StyleVu, H.-T., Tran, N., Nguyen, T.-D., Vu, Q.-L., Bui, M.-H., Le, M.-T., & Le, L. (2020). Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae. Plants, 9(1), 61. https://doi.org/10.3390/plants9010061