Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Chloroplast Genome Assembly and Features
2.2. Expansion and Contraction of the Inverted Repeat Regions
2.3. Sequence Divergence Analysis
2.4. Characterization of Repeat Sequences and SSR Polymorphisms
2.5. Phylogenetic Relationships
3. Materials and Methods
3.1. Sample Collection, Sequencing and Assembly
3.2. Whole Chloroplast Genome Annotation and Comparison
3.3. Identification of Repeat Sequences and SSRs
3.4. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
References
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Species | Genome Size (bp) | LSC Length (bp) | SSC Length (bp) | IR Length (bp) | Total GC Content (%) | Number of Genes | |||
---|---|---|---|---|---|---|---|---|---|
Total | CDS | rRNAs | tRNAs | ||||||
V. setigerum | 158,306 | 86,763 | 18,539 | 26,502 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. sempervirens var. trichophorum | 158,184 | 86,710 | 18,472 | 26,501 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. melanocarpum | 158,196 | 86,695 | 18,497 | 26,502 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. foetidum var. rectangulatum | 158,230 | 86,835 | 18,431 | 26,482 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. luzonicum | 158,652 | 87,892 | 17,674 | 26,543 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. odoratissimum var. awabuki | 158,126 | 86,718 | 18,438 | 26,485 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. brachybotryum | 157,833 | 86,809 | 18,268 | 26,378 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. henryi | 157,862 | 86,430 | 18,452 | 26,490 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. propinquum | 157,987 | 86,839 | 18,350 | 26,399 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. rhytidophyllum | 158,520 | 87,054 | 18,338 | 26,564 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. ternatum | 158,344 | 87,109 | 18,407 | 26,414 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. cinnamomifolium | 158,347 | 87,210 | 18,347 | 26,395 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. sympodiale | 158,238 | 87,118 | 18,330 | 26,395 | 38.0% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. nervosum | 157,890 | 86,715 | 18,341 | 26,417 | 38.0% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. burejaeticum | 157,913 | 86,669 | 18,274 | 26,485 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. schensianum | 157,924 | 86,681 | 18,289 | 26,477 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. farreri | 158,046 | 86,809 | 18,401 | 26,418 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. oliganthum | 158,309 | 87,038 | 18,453 | 26,409 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. hanceanum | 158,195 | 86,815 | 18,436 | 26,472 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. odoratissimum | 158,020 | 86,653 | 18,419 | 26,474 | 38.1% | 130 | 85 (6) | 8 (4) | 37 (7) |
V. opulus | 158,520 | 87,114 | 18,456 | 26,475 | 38.2% | 130 | 85 (6) | 8 (4) | 37 (7) |
S. nigra | 158,102 | 86,518 | 18,978 | 26,303 | 38.0% | 132 | 84 (6) | 8 (4) | 40 (7) |
S. javanica | 158,624 | 87,226 | 18,854 | 26,272 | 38.0% | 132 | 84 (6) | 8 (4) | 40 (7) |
S. adnata | 158,756 | 87,328 | 18,862 | 26,283 | 38.0% | 132 | 84 (6) | 8 (4) | 40 (7) |
Gene Group | Gene Name |
---|---|
Ribosomal RNAs | rrn16(×2), rrn23(×2), rrn4.5(×2), rrn5(×2) |
Transfer RNAs | trnH-GUG, trnK-UUUa, trnQ-UUG, trnS-GCU, trnGa, trnR-UCU |
trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC, trnT-GGU | |
trnS-UGA, trnG-UCC, trnfM-CAU, trnS-GGA, trnT-UGU | |
trnL-UAAa, trnF-GAA, trnV-UACa, trnM-CAU, trnW-CCA | |
trnP-UGG, trnl-CAU(×2), trnL-CAA(×2), trnV-GAC(×2) | |
trnl-GAUa(×2), trnA-UGCa(×2), trnR-ACG(×2), trnN-GUU(×2) | |
trnL-UAG, trnM-CAUx, trnT-GGUx, trnP-GGGx | |
Photosystem I | psaB, psaA, psal, psaJ, psaC |
Photosystem II | psbA, psbK, psbl, psbM, psbD, psbC, psbZz, psbB, psbT, |
psbL, psbF, psbE, psbH, psbN, psbJ | |
Cytochrome | petN, petA, petL, petG, petBa, petDa |
ATP synthase | atpA, atpFa, atpH, atpl, atpE, atpB |
Rubisco | rbcL |
NADH dehydrogenease | ndhJ, ndhK, ndhC, ndhBa(×2), ndhD, ndhE, ndhG |
ndhl, ndhAa, ndhHz | |
Ribosomal proteins (large units) | rpl33, rpl20, rpl36, rpl14, rpl16, rpl16a, rpl22z, rpl2a(×2), |
rpl23(×2), rpl32 | |
Ribosomal proteins (small units) | rps16a, rps2, rps14, rps4, rps18, rps12b (×2), rps11, rps8, |
rps7(×2), rps15, rps3, rps19 | |
RNA polymerase | rpoC2, rpoC1a, rpoB, rpoA |
Miscellaneous proteins & ATP-dependent protease subunit P | matK, clpPb |
Other genes | accD, cemA, infA, ccsA, orf188x, lhbAx |
Hypothetical proteins & Conserved reading frame | ycf3b, ycf4, ycf2(×2), ycf1Ψ |
Viburnum | Pi | Sambucus | Pi |
---|---|---|---|
noncoding regions | |||
rps15-ycf1 | 0.02502 | trnF-ndhJ | 0.02934 |
ycf4-cemA | 0.02419 | trnN-ndhF | 0.02384 |
ycf3-trnS | 0.02356 | rps2-rpoC2 | 0.02029 |
ccsA-ndhD | 0.02298 | rps18-rpl20 | 0.01687 |
rps8-rpl14 | 0.01794 | trnG-trnR | 0.01596 |
ndhF-rpl32 | 0.01691 | trnM-psbD | 0.01446 |
trnL-trnF | 0.01647 | ycf4-cemA | 0.01335 |
ndhC-trnV | 0.01548 | ndhG-ndhI | 0.01247 |
rpl32-trnL | 0.01529 | rpl32-trnL | 0.01188 |
psbZ-trnG | 0.01512 | atpI-rps2 | 0.01101 |
coding regions | |||
rps19 | 0.01193 | ycf1 | 0.00999 |
ycf1 | 0.01173 | rpl33 | 0.00912 |
rps15 | 0.01107 | rps16 | 0.00691 |
accD | 0.00870 | atpE | 0.00415 |
matK | 0.00844 | ccsA | 0.00394 |
ndhF | 0.00779 | clpP | 0.00303 |
rpl22 | 0.00753 | ycf4 | 0.00300 |
rpl33 | 0.00737 | ndhF | 0.00298 |
rbcL | 0.00730 | ndhD | 0.00288 |
clpP | 0.00705 | rpl16 | 0.00285 |
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Ran, H.; Liu, Y.; Wu, C.; Cao, Y. Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae). Plants 2020, 9, 1143. https://doi.org/10.3390/plants9091143
Ran H, Liu Y, Wu C, Cao Y. Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae). Plants. 2020; 9(9):1143. https://doi.org/10.3390/plants9091143
Chicago/Turabian StyleRan, Hang, Yanyan Liu, Cui Wu, and Yanan Cao. 2020. "Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)" Plants 9, no. 9: 1143. https://doi.org/10.3390/plants9091143
APA StyleRan, H., Liu, Y., Wu, C., & Cao, Y. (2020). Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae). Plants, 9(9), 1143. https://doi.org/10.3390/plants9091143