The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery
Abstract
1. Introduction
2. Results
2.1. Chloroplast Genome Component
2.2. Gene Function Annotation and Classification
2.3. IR Expansion and Contraction
2.4. Phylogenetic Analysis and Divergence Time Dating Among Common Sedges
2.5. Chemical Control Method
3. Discussion
4. Materials and Methods
4.1. DNA Extraction and Sequencing
4.2. Genome Assembly
4.3. Genome Component Analysis
4.4. Gene Function Annotation and Classification Analysis
4.5. Contraction and Expansion Analysis of Inverted Repeats Regions
4.6. Phylogenetic Analysis
4.7. Divergence Time Dating Analysis
4.8. Detection of Sensitivity to Common Herbicides
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Category | Gene Groups | Gene Name |
---|---|---|
Photosynthesis | Subunits_of_photosystem_I | psaA, psaB, psaC, psaI, psaJ |
Subunits_of_photosystem_II | pbf1, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ | |
Subunits_of_NADH_dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
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 | |
Self-replication | Large_subunits_of_ribosome | rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 |
Small_subunits_of_ribosome | rps11, rps12, rps14, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8 | |
DNA-dependent_RNA_polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
Ribosomal_RNAs | rrn16, rrn23, rrn4.5, rrn5 | |
Transfer_RNAs | trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA, trnfM-CAU | |
Other genes | Maturase | matK |
Protease | clpP1 | |
Envelope_membrane_protein | cemA | |
Acetyl-CoA_carboxylase | ||
C-type_cytochrome_synthesis_gene | ccsA | |
Translation_initiation_factor | ||
protochlorophillide_reductase_subunit | ||
Unknown Genes | Proteins_of_unknown_function | ycf3, ycf4 |
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Gao, Z.; Cai, Y.; Long, J.; Wang, B.; Huang, Z.; Gao, Y. The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery. Int. J. Mol. Sci. 2025, 26, 2321. https://doi.org/10.3390/ijms26052321
Gao Z, Cai Y, Long J, Wang B, Huang Z, Gao Y. The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery. International Journal of Molecular Sciences. 2025; 26(5):2321. https://doi.org/10.3390/ijms26052321
Chicago/Turabian StyleGao, Zhaoliang, Yutong Cai, Jiaqi Long, Bo Wang, Zhaofeng Huang, and Yuan Gao. 2025. "The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery" International Journal of Molecular Sciences 26, no. 5: 2321. https://doi.org/10.3390/ijms26052321
APA StyleGao, Z., Cai, Y., Long, J., Wang, B., Huang, Z., & Gao, Y. (2025). The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery. International Journal of Molecular Sciences, 26(5), 2321. https://doi.org/10.3390/ijms26052321