Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Material Collection and DNA Extraction
2.2. PCR Amplification and Sequencing of the Internal Transcribed Spacer
2.3. Plastome Sequencing, Assembly, and Annotation
2.4. Identification of the Simple Sequence Repeats
2.5. Plastome Comparison
2.6. Sliding Window Analysis and Phylogenetic Analysis
3. Results
3.1. General Characteristics of the Four Rosa Plastomes
3.2. Simple Sequence Repeat Analysis
3.3. Comparative Analysis of the Plastomes of Four Rosa Species
3.4. Nucleotide Diversity Analysis by Sliding Window
3.5. Phylogenetic Analysis
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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Primer | Sequence (5′-3′) | Direction | Temperature (°C) | Reference |
---|---|---|---|---|
ITS1nF | AGAAGTCGTAACAAGGTTTCCGTAGG | Forward | 58 | [50] |
ITS4nR | TCCTCCGCTTATTGATATGC | Reverse | 58 | [50] |
Species | Rosa acicularis | Rosa iliensis | Rosa laxa | Rosa spinosissima |
---|---|---|---|---|
GenBank accession number | PV330080 | PV330081 | PV330082 | PV330083 |
Genome size (bp) | 157,288 | 157,148 | 157,346 | 157,177 |
LSC length (bp) | 86,381 | 86,274 | 86,461 | 86,269 |
SSC length (bp) | 18,791 | 18,778 | 18,791 | 18,784 |
IRA length (bp) | 26,058 | 26,048 | 26,047 | 26,062 |
IRB length (bp) | 26,058 | 26,048 | 26,047 | 26,062 |
Total GC content (%) | 37.20 | 37.20 | 37.20 | 37.20 |
Number of total genes (unique) | 136 (116) | 136 (116) | 136 (116) | 136 (116) |
Total protein-coding genes (unique) | 90 (81) | 90 (81) | 90 (81) | 90 (81) |
Total tRNA genes (unique) | 38 (31) | 38 (31) | 38 (31) | 38 (31) |
Total rRNA genes (unique) | 8 (4) | 8 (4) | 8 (4) | 8 (4) |
Group of Genes | Name of Genes |
---|---|
Self-replication | |
Ribosomal RNA | rrn4.5 (×2), rrn5 (×2), rrn16 (×2), rrn23 (×2) |
Transfer RNA | trnA-UGC * (×2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC *, trnG-UCC, trnH-GUG, 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-CGA *, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (×2), trnV-UAC *, trnW-CCA, trnY-GUA |
Small subunit of ribosome | rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps12 ** (×2), rps14, rps15, rps16 *, rps18, rps19 |
Large subunit of ribosome | rpl2 * (×2), rpl14, rpl16 *, rpl20, rpl22, rpl23 (×2), 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 * (×2), 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 | |
Conserved hypothetical chloroplast ORF | ycf1 (×2), ycf2 (×2), ycf3 **, ycf4, ycf15 (×2), ycf68 (×2) |
Type | Repeat Unit | Rosa acicularis | Rosa iliensis | Rosa laxa | Rosa spinosissima | Total | % |
---|---|---|---|---|---|---|---|
Mono- | A/T | 138 | 144 | 138 | 143 | 563 | 66.41 |
C/G | 9 | 10 | 10 | 9 | 38 | ||
Di- | AT/AT | 39 | 39 | 39 | 38 | 155 | 24.64 |
AG/CT | 16 | 16 | 16 | 16 | 64 | ||
AC/GT | 1 | 1 | 1 | 1 | 4 | ||
Tri- | AAT/ATT | 7 | 5 | 7 | 7 | 26 | 2.98 |
AGC/CTG | 0 | 0 | 0 | 1 | 1 | ||
Tetra- | AAAT/ATTT | 6 | 6 | 6 | 6 | 24 | 4.75 |
AATT/AATT | 2 | 1 | 2 | 2 | 7 | ||
ACAT/ATGT | 1 | 1 | 1 | 1 | 4 | ||
ACCT/AGGT | 2 | 2 | 2 | 2 | 8 | ||
Penta- | AATAT/ATATT | 1 | 0 | 1 | 0 | 2 | 0.33 |
AAAAG/CTTTT | 0 | 0 | 0 | 1 | 1 | ||
Hexa- | AAGTAG/ACTTCT | 2 | 2 | 2 | 2 | 8 | 0.88 |
Total | 224 | 227 | 225 | 229 | 905 | 100.00 |
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Yermagambetova, M.; Imanbayeva, A.; Ishmuratova, M.; Sumbembayev, A.; Almerekova, S. Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences. Genes 2025, 16, 852. https://doi.org/10.3390/genes16080852
Yermagambetova M, Imanbayeva A, Ishmuratova M, Sumbembayev A, Almerekova S. Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences. Genes. 2025; 16(8):852. https://doi.org/10.3390/genes16080852
Chicago/Turabian StyleYermagambetova, Moldir, Akzhunis Imanbayeva, Margarita Ishmuratova, Aidar Sumbembayev, and Shyryn Almerekova. 2025. "Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences" Genes 16, no. 8: 852. https://doi.org/10.3390/genes16080852
APA StyleYermagambetova, M., Imanbayeva, A., Ishmuratova, M., Sumbembayev, A., & Almerekova, S. (2025). Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences. Genes, 16(8), 852. https://doi.org/10.3390/genes16080852