Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species
Abstract
:1. Introduction
2. Material and Methods
2.1. Plant Materials
2.2. DNA Extraction
2.3. Chloroplast DNA Sequencing, Assembly, and Annotation
2.4. Repeat Analysis
2.5. IR Border Region and Chloroplast Genome Comparison
2.6. Genetic Distance and Sequence Divergence Snalysis
2.7. Phylogenetic Tree Analysis
3. Results
3.1. Barleria Chloroplast Genome Organization and Features
3.2. Repeated Sequence Analysis
3.3. Comparison of Border Regions in Barleria Chloroplast Genomes
3.4. Genetic Distance Analysis
3.5. Interspecific Genome Variations and Nucleotide Diversities
3.6. Recognition of Highly Variable Regions within the Barleria Chloroplast Genomes
3.7. Phylogenetic Relationship Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
cp | chloroplast genomes |
LSC | a large single copy |
SSC | a small single copy |
IRs | a pair of inverted repeats |
CDS | protein-coding sequence |
SSR | simple sequence repeat |
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Plant Species | Length (bp) | G-C Content (%) | Total of Genes | CDS | tRNA | rRNA | Collection Numbers | GenBank Accession Numbers | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LSC | SSC | IR | cpGenome | LSC | SSC | IR | cpGenome | |||||||
B. cristata | 83,650 | 17,677 | 25,325 | 151,977 | 36.5 | 32.6 | 38.4 | 43.5 | 131 | 86 | 37 | 8 | A. Chaveerach 1095 | ON768801 |
B. lupulina | 83,854 | 17,789 | 25,315 | 152,273 | 36.4 | 32.7 | 38.3 | 43.5 | 131 | 86 | 37 | 8 | A. Chaveerach 1096 | ON768802 |
B. repens | 83,819 | 17,771 | 25,367 | 152,324 | 36.5 | 32.5 | 38.3 | 43.4 | 131 | 86 | 37 | 8 | A. Chaveerach 1099 | ON768803 |
B. siamensis | 83,929 | 17,804 | 25,296 | 152,236 | 36.5 | 32.7 | 38.4 | 43.4 | 131 | 86 | 37 | 8 | A. chaveerach 1098 | ON768804 |
B. strigosa | 83,804 | 17,715 | 25,315 | 152,272 | 36.5 | 32.4 | 38.3 | 43.5 | 131 | 86 | 37 | 8 | A. chaveerach 1097 | ON768805 |
Category | Group of Function | Location | List of Genes |
---|---|---|---|
Self-replication related genes | Large subunit of ribosome proteins | LSC/IR/SSC | rpl2(x2) b, rpl14, rpl16 b, rpl20, rpl22, rpl23(x2), rpl32, rpl33, rpl36 |
small subunit of ribosomal proteins | LSC/IR/SSC | rps2, rps3, rps4, rps7(x2), rps8, rps11, rps12 a, rps14, rps15, rps16 b, rps18, rps19 | |
DNA-dependent RNA polymerase | LSC | rpoA, rpoB, rpoC1 b, rpoC2 | |
rRNA genes | IR | rrn4.5(x2), rrn5(x2), rrn16(x2), rrn23(x2) b | |
tRNA genes | LSC/IR/SSC | trnA-UGC(x2) b, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnH-GUG, trnI-CAU(x2), trnI-GAU(x2) b, trnK-UUU b, trnL-CAA(x2), trnL-UAA b, trnL-UAG, trnM-CAU, trnN-GUU(x2), trnP-UGG, trnQ-UUG, trnR-ACG(x2), trnR-UCU, trnS-CGA b, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(x2), trnV-UAC b, trnW-CCA, trnY-GUA | |
Photosynthesis related genes | Photosystem I | LSC/SSC | psaA, psaB, psaC, psaI, psaJ |
Photosystem II | LSC | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
NADH oxidoreductase | LSC/IR/SSC | ndhA b, ndhB(x2) b, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Cytochrome b6/f complex | LSC | petA, petB b, petD b, petG, petL, petN | |
Cytochrome c synthesis | SSC | ccsA | |
ATP synthase | LSC | atpA, atpB, atpE, atpF b, atpH, atpI | |
Rubisco | LSC | rbcL | |
Other genes | Maturase | LSC | matK |
Protease | LSC | clpP c | |
Envelope membrane protein | LSC | cemA | |
Subunit acetyl-CoA-carboxylase | LSC | accD | |
translational initiation factor 1 | LSC | infA | |
Unknown function genes | Conserved hypothetical chloroplast reading frames (ycf) | LSC/IR/SSC | ycf1, ycf2(x2), ycf3 c, ycf4, ycf15(x2) |
List of Genes | Location | Size (bp) | Total Size (bp) | ||||
---|---|---|---|---|---|---|---|
Exon I | Intron I | Exon II | Intron II | Exon III | |||
atpF | LSC | 446 | 698 | 143 | 1289 | ||
clpP | LSC | 228 | 642 | 291 | 718 | 66 | 1948 |
ndhA | SSC | 539 | 1071 | 551 | 2163 | ||
ndhB | IR | 755 | 678 | 776 | 2211 | ||
petB | LSC | 5 | 735 | 641 | 1383 | ||
petD | LSC | 7 | 742 | 474 | 1225 | ||
rpl16 | LSC | 405 | 893 | 8 | 1308 | ||
rpl2 | IR | 392 | 671 | 434 | 1499 | ||
rpoC1 | LSC | 1621 | 797 | 430 | 2851 | ||
rps16 | LSC | 226 | 867 | 39 | 1134 | ||
rrn23 | IR | 198 | 2611 | 2810 | |||
trnA-UGC | IR | 35 | 810 | 36 | 883 | ||
trnI-GAU | IR | 41 | 939 | 34 | 1016 | ||
trnK-UUU | LSC | 36 | 2452 | 36 | 2525 | ||
trnL-UAA | LSC | 36 | 485 | 49 | 572 | ||
trnS-CGA | LSC | 31 | 664 | 59 | 756 | ||
trnV-UAC | LSC | 36 | 592 | 37 | 667 | ||
ycf3 | LSC | 154 | 727 | 226 | 695 | 127 | 1933 |
B. strigosa | B. repens | B. cristata | B. siamensis | B. prionitis | B. lupulina | |
---|---|---|---|---|---|---|
B. strigosa | 1.00 | |||||
B. repens | 0.00574 | 1.00 | ||||
B. cristata | 0.00601 | 0.00374 | 1.00 | |||
B. siamensis | 0.00813 | 0.00772 | 0.00792 | 1.00 | ||
B. prionitis | 0.01125 | 0.01097 | 0.01109 | 0.01109 | 1.00 | |
B. lupulina | 0.01031 | 0.00990 | 0.01016 | 0.00998 | 0.00241 | 1.00 |
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Kaewdaungdee, S.; Sudmoon, R.; Tanee, T.; Lee, S.Y.; Chaveerach, A. Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species. Genes 2022, 13, 1705. https://doi.org/10.3390/genes13101705
Kaewdaungdee S, Sudmoon R, Tanee T, Lee SY, Chaveerach A. Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species. Genes. 2022; 13(10):1705. https://doi.org/10.3390/genes13101705
Chicago/Turabian StyleKaewdaungdee, Sanit, Runglawan Sudmoon, Tawatchai Tanee, Shiou Yih Lee, and Arunrat Chaveerach. 2022. "Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species" Genes 13, no. 10: 1705. https://doi.org/10.3390/genes13101705
APA StyleKaewdaungdee, S., Sudmoon, R., Tanee, T., Lee, S. Y., & Chaveerach, A. (2022). Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species. Genes, 13(10), 1705. https://doi.org/10.3390/genes13101705