Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan
Abstract
:1. Introduction
2. Results
2.1. Features of the Plastid Genome
2.2. Plastome Analysis by Sliding Window
2.3. IR and SC Regions Boundary Analysis
2.4. Repeat Sequence Analysis
2.5. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials and DNA Extraction
4.2. Genome Sequencing, Assembly, and Annotation
4.3. Plastome Analysis by Sliding Window, Ka/Ks Calculation, IR Regions Contraction, and Expansion
4.4. Repeat Sequence Analysis
4.5. Phylogenetic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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C. orientale | C. nitrarium | C. dzhungaricum | C. laricinum | |
---|---|---|---|---|
GenBank numbers | OR551471 | OR552116 | PP503423 | PP503424 |
Genome size (bp) | 151,307 | 150,777 | 151,148 | 151,115 |
LSC (bp) | 83,693 | 83,329 | 83,706 | 83,678 |
SSC (bp) | 18,266 | 18,986 | 18,996 | 18,999 |
IR (bp) | 51,348 | 48,462 | 48,446 | 48,438 |
Number of total genes | 133 | 133 | 133 | 133 |
Protein-coding genes | 80 | 80 | 80 | 80 |
tRNAs | 30 | 30 | 30 | 30 |
rRNAs | 4 | 4 | 4 | 4 |
Total GC content (%) | 36.69 | 36.84 | 36.68 | 36.71 |
LSC GC content (%) | 34.69 | 34.86 | 34.67 | 34.69 |
SSC GC content (%) | 29.68 | 30.33 | 28.80 | 29.82 |
IR GC content (%) | 42.57 | 42.60 | 42.70 | 42.72 |
Category | Group of Genes | Name of Genes |
---|---|---|
Self-replication | Ribosomal RNA | rrn4.5 (x2), rrn5 (x2), rrn16 (x2), rrn23 (x2) |
Transfer RNA | trnA-UGC * (x2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC *, trnG-UCC, trnH-GUG, trnI-CAU (x2), trnI-GAU * (x2), trnK-UUU *, trnL-CAA (x2), trnL-UAA *, trnL-UAG, trnM-CAU, trnN-GUU (x2), trnP-UGG, trnQ-UUG, trnR-ACG (x2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (x2), trnV-UAC *, trnW-CCA, trnY-GUA | |
Small subunit of ribosome | rps2, rps3, rps4, rps7 (x2), rps8, rps11, rps12 * (x2), rps14, rps15, rps16 *, rps18, rps19 | |
Large subunit of ribosome | rpl2 (x2), rpl14, rpl16 *, rpl20, rpl22, rpl23 (x2), rpl32, rpl33, rpl36 | |
RNA polymerase | rpoA, rpoB, rpoC1 *, rpoC2 | |
Translation initiation factor | infA | |
Photosynthesis | ATP synthase | atpA, atpB, atpE, atpF *, atpH, atpI |
NADH dehydrogenase | ndhA *, ndhB * (x2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Subunits of cytochrome | petA, petB *, petD *, petG, petL, petN | |
Photosystem I | psaA, psaB, psaC, psaI, psaJ | |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Rubisco | rbcL | |
Other genes | Maturase | matK |
Protease | clpP ** | |
Envelope membrane protein | cemA | |
Subunit of acetyl-CoA-carboxylase | accD | |
C-type cytochrome synthesis gene | ccsA | |
Genes of unknown function | Hypothetical chloroplast reading frames | ycf1 (x2), ycf2 (x2), ycf3 **, ycf4, ycf15 (x2) |
Variable Region | Length | Variable Sites | Parsimony Informative Sites | Nucleotide Diversity | Analysed Genes | Ka/Ks Ratio |
---|---|---|---|---|---|---|
accD | 723 | 103 | 36 | 0.05063 | accD | 0.900 |
atpF | 771 | 75 | 35 | 0.04170 | atpF | 1.308 |
matK | 606 | 96 | 37 | 0.05111 | matK | 1.813 |
ndhF-ndhG | 606 | 101 | 44 | 0.05459 | ndhF ndhG | 0.600 0.476 |
petB | 721 | 84 | 36 | 0.04252 | petB | 4.139 |
rpl20-rpl22 | 606 | 114 | 43 | 0.05711 | rpl20 rpl22 | 1.099 2.425 |
rpoC2 | 606 | 78 | 32 | 0.04141 | rpoC2 | 0.476 |
ycf3 | 672 | 77 | 34 | 0.04185 | ycf3 | 1.104 |
Type | Repeat Unit | C. orientale | C. nitrarium | C.dzhungaricum | C. laricinum | Total (%) | % |
---|---|---|---|---|---|---|---|
Mono- | A/T | 148 | 137 | 149 | 147 | 581 (97.81) | 72.97 |
C/G | 3 | 4 | 3 | 3 | 13 (2.19) | ||
Di- | AC/GT | 2 | 4 | 2 | 2 | 10 (6.45) | 19.04 |
AG/CT | 15 | 15 | 15 | 15 | 60 (38.71) | ||
AT/AT | 20 | 25 | 21 | 19 | 85 (54.84) | ||
Tri- | AAG/CTT | - | 2 | 2 | 2 | 6 (24) | 3.07 |
AAT/ATT | 5 | 4 | 5 | 5 | 19 (76.00) | ||
Tetra- | AAAC/GTTT | 1 | 1 | 1 | 1 | 4 (11.76) | 4.18 |
AAAG/CTTT | 3 | - | 3 | 2 | 8 (23.53) | ||
AAAT/ATTT | 1 | 1 | 1 | 1 | 4 (11.76) | ||
AAGG/CCTT | - | 1 | - | - | 1 (2.94) | ||
AATC/ATTG | - | - | 1 | - | 1 (2.94) | ||
AATT/AATT | 2 | 2 | 2 | 2 | 8 (23.53) | ||
ACCT/AGGT | 2 | 2 | 2 | 2 | 8 (23.53) | ||
Penta- | AAAAG/CTTTT | 1 | - | 1 | 1 | 3 (75.00) | 0.49 |
AAAGG/CCTTT | 1 | - | - | - | 1 (25.00) | ||
Hexa- | AGCTCC/AGCTGG | - | - | - | 2 | 2 (100.00) | 0.25 |
Total | 204 | 198 | 208 | 204 | 814 (100) | 100 |
Species | Collected Place | GPS Coordinates |
---|---|---|
C. orientale | Kyzylorda region, Zhanakorgan district. | 44.106111, 67.062778 150 m above sea level (m a. s. l.) |
C. nitrarium | Kyzylorda region, Zhanakorgan district. | 44.110833, 67.061111 150 m a. s. l. |
C. dzhungaricum | Almaty region, Trans-Ili Alatau, left bank of the Charyn river. | 43.249722, 78.898611 1210 m a. s. l. |
C. laricinum | West Kazakhstan region, Burlinsky district, Bestau village. | 51.254444, 53.093611 120 m a. s. l. |
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Almerekova, S.; Yermagambetova, M.; Osmonali, B.; Vesselova, P.; Abugalieva, S.; Turuspekov, Y. Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan. Plants 2024, 13, 1332. https://doi.org/10.3390/plants13101332
Almerekova S, Yermagambetova M, Osmonali B, Vesselova P, Abugalieva S, Turuspekov Y. Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan. Plants. 2024; 13(10):1332. https://doi.org/10.3390/plants13101332
Chicago/Turabian StyleAlmerekova, Shyryn, Moldir Yermagambetova, Bektemir Osmonali, Polina Vesselova, Saule Abugalieva, and Yerlan Turuspekov. 2024. "Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan" Plants 13, no. 10: 1332. https://doi.org/10.3390/plants13101332