Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species
Abstract
:1. Introduction
2. Results and Discussion
2.1. Features of the Cp Genome of Mainland A. Spathulifolius
2.1.1. General Structure and Gene Contents
2.1.2. Codon Usage and Prediction of RNA-Editing Sites
2.2. Comparative Analysis of the Cp Genomes in the Aster Genus
2.2.1. General Features of the Aster Cp Genomes
2.2.2. Cp Genome Sequence Conservation and Divergence
2.2.3. Gene-By-Gene Sequence Divergence
2.2.4. Contraction and Expansion of the IR Region
2.2.5. Repeat Sequence Analysis
2.2.6. Phylogenetic Studies
2.2.7. Positive Selected Analysis
3. Materials and Methods
3.1. Ethics Statement
3.2. Sample Collection and Sequencing
3.3. Cp Genome Assembly, Annotation, and Sequence Analysis
3.4. Comparative Genomic Analysis and Evaluation of highly Divergent Regions
3.5. Characterization of Repeat Sequences
3.6. Phylogenetic Analysis
3.7. Positive Selected Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Category | T/U (%) | C (%) | A (%) | G (%) | Length (bp) |
---|---|---|---|---|---|
Genome | 31.53 | 18.37 | 31.19 | 18.91 | 152,732 |
LSC | 32.61 | 17.27 | 32.23 | 17.88 | 84,552 |
SSC | 34.87 | 14.82 | 33.81 | 16.50 | 18,268 |
IRa | 28.62 | 20.79 | 28.32 | 22.28 | 24,956 |
IRb | 28.32 | 22.28 | 28.62 | 20.79 | 24,956 |
tRNA genes | 25.00 | 23.56 | 22.09 | 29.35 | 2784 |
rRNA genes | 18.79 | 23.63 | 26.04 | 31.54 | 9048 |
Protein-coding genes | 31.45 | 17.72 | 30.53 | 20.31 | 78,654 |
1st position | 23.82 | 18.87 | 30.51 | 26.80 | 26,218 |
2nd position | 32.58 | 20.31 | 29.30 | 17.81 | 26,218 |
3rd position | 37.93 | 13.98 | 31.78 | 16.31 | 26,218 |
Category | Group of Genes | Name of Genes |
---|---|---|
Self-replication | Large subunit of ribosomal proteins | rpl2 * (2x), 14, 16 *, 20, 22, 23(2x), 32, 33, 36 |
Small subunit of ribosomal proteins | rps2, 3, 4, 7(2x), 8, 11, 12 ** (2x), 14, 15, 16 *, 18, 19 | |
DNA dependent RNA polymerase | rpoA, B, C1 *, C2 | |
rRNA genes | rrn16S(2x) , rrn23S(2x), rrn4.5S(2x), rrn5S(2x) | |
tRNA genes | trnA-UGC * (2x), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC *, trnH-GUG, trnI-CAU(2x), trnI-GAU * (2x), trnK-UUU *, trnL-CAA(2x), trnL-UAA *, trnL-UAG, trnM-CAU, trnN-GUU(2x), trnP-UGG, trnQ-UUG, trnR-ACG(2x), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2x), trnV-UAC *, trnW-CCA, trnY-GUA | |
Photosynthesis | Photosystem I | psaA, B, C, I, J |
Photosystem II | PsbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z | |
NADH dehydrogenase | ndhA *, B * (2x), 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 | |
Other genes | Translational initiation factor | infA |
Maturase | matK | |
Protease | clpP * | |
Envelop membrane protein | cemA | |
Subunit acetyl-CoA carboxylase | accD | |
C-type cytochrome synthesis gene | ccsA | |
Unknown | Conserved open reading frame | ycf1, 2(2x), 3 *, 4, 15(2x) |
Amino Acid | Codon | No | RSCU | tRNA | Amino Acid | Codon | No | RSCU | tRNA |
---|---|---|---|---|---|---|---|---|---|
Phe | UUU | 983 | 1.31 | Thr | ACU | 529 | 1.61 | ||
Phe | UUC | 516 | 0.69 | trnF-GAA | Thr | ACC | 238 | 0.73 | trnT-GGU |
Leu | UUA | 865 | 1.84 | trnL-UAA | Thr | ACA | 406 | 1.24 | trnT-UGU |
Leu | UUG | 588 | 1.25 | trnL-CAA | Thr | ACG | 138 | 0.42 | |
Leu | CUU | 607 | 1.29 | Ala | GCU | 624 | 1.74 | ||
Leu | CUC | 194 | 0.41 | Ala | GCC | 236 | 0.66 | ||
Leu | CUA | 379 | 0.81 | trnL-UAG | Ala | GCA | 408 | 1.14 | trnA-UGC |
Leu | CUG | 182 | 0.39 | Ala | GCG | 166 | 0.46 | ||
Ile | AUU | 1074 | 1.47 | Tyr | UAU | 802 | 1.64 | ||
Ile | AUC | 427 | 0.58 | trnI-GAU | Tyr | UAC | 177 | 0.36 | trnY-GUA |
Ile | AUA | 689 | 0.94 | STOP | UAA | 51 | 1.76 | ||
Met | AUG | 635 | 1.00 | trn(f)M-CAU | STOP | UAG | 21 | 0.72 | |
Val | GUU | 511 | 1.46 | STOP | UGA | 15 | 0.52 | ||
Val | GUC | 178 | 0.51 | trnV-GAC | His | CAU | 457 | 1.50 | |
Val | GUA | 524 | 1.49 | trnV-UAC | His | CAC | 153 | 0.50 | trnH-GUG |
Val | GUG | 191 | 0.54 | Gln | CAA | 727 | 1.53 | trnQ-UUG | |
Ser | UCU | 590 | 1.77 | Gln | CAG | 221 | 0.47 | ||
Ser | UCC | 311 | 0.93 | trnS-GGA | Asn | AAU | 973 | 1.53 | |
Ser | UCA | 403 | 1.21 | trnS-UGA | Asn | AAC | 298 | 0.47 | trnN-GUU |
Ser | UCG | 169 | 0.51 | Lys | AAA | 1034 | 1.48 | trnK-UUU | |
Ser | AGU | 401 | 1.21 | Lys | AAG | 366 | 0.52 | ||
Ser | AGC | 122 | 0.37 | trnS-GCU | Asp | GAU | 851 | 1.61 | |
Arg | AGA | 495 | 1.87 | trnR-UCU | Asp | GAC | 209 | 0.39 | trnD-GUC |
Arg | AGG | 174 | 0.66 | Glu | GAA | 990 | 1.48 | trnE-UUC | |
Arg | CGU | 353 | 1.33 | trnR-ACG | Glu | GAG | 352 | 0.52 | |
Arg | CGC | 109 | 0.41 | Cys | UGU | 207 | 1.41 | ||
Arg | CGA | 346 | 1.31 | Cys | UGC | 86 | 0.59 | trnC-GCA | |
Arg | CGG | 113 | 0.43 | Trp | UGG | 462 | 1.00 | trnW-CCA | |
Pro | CCU | 409 | 1.48 | Gly | GGU | 574 | 1.29 | ||
Pro | CCC | 211 | 0.76 | Gly | GGC | 199 | 0.45 | trnG-GCC | |
Pro | CCA | 316 | 1.14 | trnP-UGG | Gly | GGA | 684 | 1.53 | trnG-UCC |
Pro | CCG | 170 | 0.61 | Gly | GGG | 329 | 0.74 |
Attributes | Mainland A. spathulifolius | Island A. spathulifolius | A. altaicus | A. hersileoides | A. indicus | A. tataricus |
---|---|---|---|---|---|---|
Size (bp) | 152,732 | 149,473 | 152,446 | 152,345 | 152,885 | 152,992 |
GC content (%) | 37.2 | 37.7 | 37.3 | 37.3 | 37.0 | 37.3 |
LSC size (bp) | 84,552 | 81,998 | 84,240 | 84,124 | 84,610 | 84,698 |
SSC size (bp) | 18,268 | 17,973 | 18,196 | 18,243 | 18,269 | 18,250 |
IR size (bp) | 24,956 | 24,751 | 25,005 | 24,989 | 25,003 | 25,022 |
No. of genes | 114 | 114 | 114 | 114 | 114 | 114 |
Protein-coding genes | 80 | 80 | 80 | 80 | 80 | 80 |
tRNA genes | 30 | 30 | 30 | 30 | 30 | 30 |
rRNA genes | 4 | 4 | 4 | 4 | 4 | 4 |
Genes duplicated | 18 | 18 | 18 | 18 | 18 | 18 |
Genes with intron | 17 | 17 | 17 | 17 | 17 | 17 |
Pseudogene | 3 | 3 | 2 | 2 | 2 | 2 |
Genes | Location | Mainland A. spathulifolius | Island A. spathulifolius | Aster altaicus | Aster hersileoides | Aster indicus | Aster tataricus | |
---|---|---|---|---|---|---|---|---|
atpF | LSC | 715 | 699 | 709 | 709 | 709 | 718 | |
clpP | Intron1 Intron2 | LSC | 812 | 800 | 812 | 811 | 814 | 812 |
616 | 623 | 614 | 615 | 615 | 614 | |||
ndhA | SSC | 1064 | 1105 | 1046 | 1077 | 1064 | 1055 | |
ndhB | IR | 676 | 670 | 674 | 674 | 674 | 674 | |
petB | LSC | 840 | 745 | 798 | 796 | 823 | 830 | |
petD | LSC | 767 | 724 | 760 | 785 | 809 | 745 | |
rpl16 | LSC | 1058 | 1017 | 1087 | 1053 | 1098 | 1144 | |
rpl2 | IR | 671 | 671 | 671 | 671 | 671 | 671 | |
rpoC1 | LSC | 742 | 721 | 743 | 742 | 742 | 743 | |
rps12 | 535 | 535 | 535 | 535 | 535 | 535 | ||
rps16 | LSC | 887 | 817 | 890 | 877 | 876 | 885 | |
ycf3 | Intron1 Intron2 | LSC | 692 | 697 | 691 | 690 | 702 | 690 |
744 | 739 | 739 | 739 | 739 | 739 | |||
trnA-UGC | IR | 820 | 820 | 819 | 820 | 820 | 820 | |
trnG-UCC | LSC | 732 | 722 | 732 | 733 | 732 | 732 | |
trnI_GAU | IR | 780 | 781 | 780 | 775 | 780 | 781 | |
trnK-UUU | LSC | 2542 | 2502 | 2528 | 2538 | 2539 | 2535 | |
trnL-UAA | LSC | 438 | 423 | 438 | 438 | 438 | 438 | |
trnV-UAC | LSC | 573 | 573 | 573 | 573 | 573 | 573 |
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Tyagi, S.; Jung, J.-A.; Kim, J.S.; Won, S.Y. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. Plants 2020, 9, 568. https://doi.org/10.3390/plants9050568
Tyagi S, Jung J-A, Kim JS, Won SY. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. Plants. 2020; 9(5):568. https://doi.org/10.3390/plants9050568
Chicago/Turabian StyleTyagi, Swati, Jae-A Jung, Jung Sun Kim, and So Youn Won. 2020. "Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species" Plants 9, no. 5: 568. https://doi.org/10.3390/plants9050568