The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)
Abstract
:1. Introduction
2. Results
2.1. Chloroplast Genome Structure
2.2. Sequence Divergence in the Zoysia Chloroplast Genomes
2.3. Simple Sequence Repeats
2.4. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials, DNA Extraction, and Sequencing
4.2. Chloroplast Genome Assembly and Annotation
4.3. Sequence Analysis
4.4. Phylogenetic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
LSC | Large Single Copy |
SSC | Small Single Copy |
IR | Inverted Repeat |
SSR | Simple Sequence Repeat |
ML | Maximum Likelihood |
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Species | Zoysia japonica | Zoysia tenuifolia | Zoysia sinica | Zoysia macrostachya | Zoysia matrella * | Zoysia macrantha * |
---|---|---|---|---|---|---|
Accession number | MF953592 | MF967580 | MF967579 | MF967581 | AP014937 | KT168390 |
Genome length (bp) | 135,854 | 135,892 | 135,872 | 135,904 | 135,810 | 135,845 |
LSC length (bp) | 81,348 | 81,376 | 81,366 | 81,392 | 81,308 | 81,352 |
SSC length (bp) | 12,582 | 12,584 | 12,582 | 12,586 | 12,583 | 12,576 |
IR length (bp) | 20,962 | 20,966 | 20,962 | 20,963 | 20,960 | 20,959 |
AT content | 61.6% | 61.6% | 61.6% | 61.6% | 61.6% | 61.6% |
Total gene contents | 110 | 110 | 110 | 110 | 110 | 110 |
Genes Category | Group of Genes | Name of Genes |
---|---|---|
Self-replication | rRNA genes | rrn16 (x2), rrn23 (x2), rrn4.5 (x2), rrn5 (x2) |
tRNA genes | 30 trn genes (8 are in IR regions) | |
Small subunit of ribosome | rps2, rps3, rps4, rps7 (x2), rps8, rps11, rps12 * (x2), rps14, rps15 (x2), rps16 *, rps18, rps19 (x2) | |
Large subunit of ribosome | rpl2 * (x2), rpl14, rpl16 *, rpl20, rpl22, rpl23 (x2), rpl32, rpl33, rpl36 | |
DNA dependent RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
Genes for photosynthesis | Subunits of NADH-dehydrogenase | ndhA *, ndhB * (x2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
Subunits of photosystem 1 | psaA, psaB, psaC, psaI, psaJ | |
Subunits of photosystem 2 | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Subunits of cytochrome b/f complex | petA, petB *, petD *, petG, petL, petN | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF *, atpH, atpI | |
Large subunit of rubisco | rbcL | |
Other genes | Maturase | matK |
Protease | clpP | |
Envelope membrane protein | cemA | |
c-type cytochrome synthesis gene | ccsA | |
Translational initiation factor | infA | |
Genes of unknown functions Open Reading Frames (ORF) | ycf3 **, ycf4 |
Unit | Length (bp) | Zoysia japonica | Zoysia sinica | Zoysia macrostachya | Zoysia tenuifolia |
---|---|---|---|---|---|
No. of SSRs | No. of SSRs | No. of SSRs | No. of SSRs | ||
A | 17 | 0 | 1 | 0 | 0 |
16 | 2 | 1 | 1 | 3 | |
15 | 1 | 0 | 0 | 1 | |
14 | 2 | 3 | 0 | 1 | |
13 | 2 | 2 | 3 | 3 | |
12 | 3 | 3 | 6 | 3 | |
11 | 4 | 4 | 6 | 6 | |
10 | 10 | 9 | 7 | 9 | |
C | 11 | 1 | 1 | 0 | 0 |
10 | 0 | 0 | 0 | 1 | |
G | 11 | 0 | 0 | 0 | 1 |
10 | 1 | 1 | 2 | 0 | |
T | 22 | 1 | 0 | 0 | 1 |
17 | 0 | 4 | 0 | 0 | |
16 | 0 | 0 | 1 | 0 | |
14 | 0 | 0 | 2 | 1 | |
13 | 3 | 4 | 4 | 4 | |
12 | 7 | 7 | 5 | 7 | |
11 | 5 | 6 | 4 | 7 | |
10 | 8 | 8 | 12 | 6 | |
AT | 12 | 1 | 1 | 1 | 1 |
10 | 3 | 3 | 3 | 3 | |
GA | 10 | 1 | 1 | 1 | 1 |
TA | 14 | 1 | 1 | 1 | 1 |
10 | 1 | 1 | 1 | 1 | |
TC | 10 | 1 | 1 | 1 | 1 |
AAT | 12 | 1 | 1 | 1 | 1 |
Total | 59 | 63 | 62 | 63 |
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Cheon, S.-H.; Woo, M.-A.; Jo, S.; Kim, Y.-K.; Kim, K.-J. The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae). Plants 2021, 10, 1517. https://doi.org/10.3390/plants10081517
Cheon S-H, Woo M-A, Jo S, Kim Y-K, Kim K-J. The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae). Plants. 2021; 10(8):1517. https://doi.org/10.3390/plants10081517
Chicago/Turabian StyleCheon, Se-Hwan, Min-Ah Woo, Sangjin Jo, Young-Kee Kim, and Ki-Joong Kim. 2021. "The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)" Plants 10, no. 8: 1517. https://doi.org/10.3390/plants10081517