Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples, DNA Isolation, and Sequencing
2.2. Chloroplast Genome Assembly and Annotation
2.3. Comparative Genome Analysis
2.4. Repeat and SSR Identification
2.5. Phylogenetic Analysis
2.6. Gene Selective Pressure Analysis
2.7. Development of Species-Specific Molecular Markers for Ceriops Species
3. Results
3.1. Chloroplast Genome Features
3.2. Comparative Analysis of Chloroplast Genomes
3.3. Chloroplast Boundary Structures
3.4. Chloroplast Repeats and SSRs
3.5. Ceriops Species Identification Based on Species-Specific Molecular Markers
3.6. Phylogenetic Relationships
3.7. Chloroplast Genes under Positive Selection
4. Discussion
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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Genome and Gene Features | C. decandra | C. zippeliana | C. tagal | A. lanata |
---|---|---|---|---|
Genome size (bp) | 166,650 | 166,083 | 164,432 | 148,264 |
LSC (bp) | 94,635 | 95,217 | 92,660 | 87,995 |
SSC (bp) | 18,945 | 18,054 | 19,158 | 17,949 |
IR (bp) | 26,535 | 26,406 | 26,307 | 21,160 |
LSC GC content (%) | 32.07 | 31.67 | 32.59 | 36.77 |
SSC GC content (%) | 29.28 | 29.63 | 29.31 | 32.72 |
IR GC content (%) | 41.90 | 41.86 | 42.17 | 44.26 |
Genome GC content (%) | 34.89 | 34.69 | 35.28 | 38.42 |
No. of total genes | 129 | 129 | 129 | 125 |
No. of protein coding genes | 84 | 83 | 84 | 81 |
No. of rRNAs | 8 | 8 | 8 | 8 |
No. of tRNAs | 37 | 38 | 37 | 36 |
No. of duplicated genes | 17 | 17 | 17 | 13 |
Pseudogenes | 1 (rps19) | 1 (rps19) | 1 (rps19) | 3 (rpl16, rps16, ycf2) |
Gene gain/loss | - | −rpl32 | - | +infA |
Category | Group of Genes | Gene Name |
---|---|---|
Photosynthesis | Subunits of Photosystem I | psaA, B, C, I, J |
Subunits of Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z | |
Subunits of NADH dehydrogenase | ndhA *, B *(×2), C, D, E, F, G, H, I, J, K | |
Cytochrome b6/f complex | petA, B *, D *, G, L, N | |
ATP synthase | atpA, B, E, F *, H, I | |
Rubisco | rbcL | |
Self-replication | Large subunit of ribosomal proteins | rpl2 *(×2), 14, 16 *, e, 20, 22, 23(×2), 32b, 33, 36 |
Small subunit of ribosomal proteins | rps2, 3, 4, 7(×2), 8, 11, 12 **(×2), 14, 15, 16d, 18, 19 | |
DNA dependent RNA polymerase | rpoA, B, C1 *, C2 | |
rRNA genes | rrn4.5(×2), 5(×2), 16(×2), 23 *(×2) | |
tRNA genes | trnA-UGC *(×2), trnC-ACA *, trnC-GCA, trnD-GUC, | |
trnE-UUC *(×3), trnF-GAA, trnG-GCC, trnH-GUG, | ||
trnK-UUU *, trnL-CAA(×2), trnL-UAA *, trnL-UAG, | ||
trnM-CAU(×4), trnN-GUU(×2), trnP-UGG, | ||
trnQ-UUG, trnR-ACG(×2), trnR-UCU, trnS-GCU, | ||
trnS-GGA, trnS-UGA, trnT-CGU *, trnT-GGU, | ||
trnT-UGU, trnV-GAC(×2), trnW-CCA, trnY-AUAa | ||
trnY-GUA | ||
Other genes | Maturase | matK |
Subunit Acetyl-CoA-Carboxylate | accD | |
Envelop membrane protein | cemA | |
Protease | clpP ** | |
C-type cytochrome synthesis gene | ccsA | |
Translation initiation factor gene | infAd | |
Unknown | Conserved open reading frames | ycf1, 2 (×2) e, 3 **, 4 |
Pseudogene | rps19c, rps16f, rpl16f, ycf2f |
Species | SSR Type | Total Number | The Number of SSRs for Compound Formation | |||||
---|---|---|---|---|---|---|---|---|
Mono- | Di- | Tri- | Tetra- | Penta- | Hexa- | |||
CD | 74 | 25 | 14 | 21 | 5 | 3 | 142 | 36 |
CZ | 78 | 40 | 21 | 29 | 7 | 2 | 177 | 64 |
CT | 81 | 17 | 20 | 23 | 4 | 1 | 146 | 35 |
CT a | 79 | 16 | 20 | 22 | 4 | 1 | 142 | 35 |
CT b | 78 | 16 | 20 | 23 | 4 | 1 | 142 | 35 |
AL | 38 | 2 | 3 | 7 | 0 | 0 | 50 | 5 |
AM a | 34 | 2 | 2 | 6 | 0 | 0 | 44 | 1 |
AM b | 49 | 1 | 4 | 7 | 0 | 0 | 61 | 4 |
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Ruang-areerate, P.; Yoocha, T.; Kongkachana, W.; Phetchawang, P.; Maknual, C.; Meepol, W.; Jiumjamrassil, D.; Pootakham, W.; Tangphatsornruang, S. Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. Biology 2022, 11, 383. https://doi.org/10.3390/biology11030383
Ruang-areerate P, Yoocha T, Kongkachana W, Phetchawang P, Maknual C, Meepol W, Jiumjamrassil D, Pootakham W, Tangphatsornruang S. Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. Biology. 2022; 11(3):383. https://doi.org/10.3390/biology11030383
Chicago/Turabian StyleRuang-areerate, Panthita, Thippawan Yoocha, Wasitthee Kongkachana, Phakamas Phetchawang, Chatree Maknual, Wijarn Meepol, Darunee Jiumjamrassil, Wirulda Pootakham, and Sithichoke Tangphatsornruang. 2022. "Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests" Biology 11, no. 3: 383. https://doi.org/10.3390/biology11030383
APA StyleRuang-areerate, P., Yoocha, T., Kongkachana, W., Phetchawang, P., Maknual, C., Meepol, W., Jiumjamrassil, D., Pootakham, W., & Tangphatsornruang, S. (2022). Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. Biology, 11(3), 383. https://doi.org/10.3390/biology11030383