Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and DNA Extraction
2.2. Genome Sequencing and Annotation
2.3. Sequence and Repeat Analysis
2.4. Genome Comparison and Sequence Divergence
2.5. Phylogenetic Analysis
3. Result
3.1. Structures and Features of M. shiluensis Chloroplast Genome
3.2. Codon Usage and RNA Analysis
3.3. Repeat Sequence Analysis
3.4. Genome Comparison and Sequence Divergence
3.5. Phylogenetic Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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M. shiluensis | M. odora | M. laevifolia | M. insignis | M. cathcartii | |
---|---|---|---|---|---|
Accession | MN418056 | NC023239 | NC035956 | NC035657 | NC023234 |
Genome | |||||
Length (bp) | 160,075 | 160,070 | 160,120 | 160,117 | 159,950 |
GC (%) | 39.26 | 39.26 | 39.24 | 39.24 | 39.22 |
LSC | |||||
length (bp) | 88,105 | 88,098 | 88,145 | 88,195 | 88,142 |
GC (%) | 37.95 | 37.95 | 37.9 | 37.92 | 37.91 |
Length (%) | 55.04 | 55.04 | 55.05 | 55.08 | 55.11 |
SSC | |||||
length (bp) | 18,796 | 18,800 | 18,799 | 18,782 | 18,790 |
GC (%) | 34.28 | 34.28 | 34.32 | 34.25 | 34.13 |
Length (%) | 11.74 | 11.74 | 11.74 | 11.73 | 11.75 |
IR | |||||
length (bp) | 26,587 | 26,586 | 26,588 | 26,570 | 26,509 |
GC (%) | 43.2 | 43.2 | 43.2 | 43.19 | 43.2 |
Length (%) | 16.61 | 16.61 | 16.61 | 16.59 | 16.57 |
No. of Genes (duplicated in IR) | |||||
Genes | 131(18) | 131(18) | 131(18) | 131(18) | 131(18) |
PCGs | 86(7) | 86(7) | 86(7) | 86(7) | 86(7) |
tRNA | 37(7) | 37(7) | 37(7) | 37(7) | 37(7) |
rRNA | 8(4) | 8(4) | 8(4) | 8(4) | 8(4) |
With introns | 16(5) | 16(5) | 16(5) | 16(5) | 16(5) |
Category of Genes | Subcategory of Genes | Gene Names | |||
---|---|---|---|---|---|
Self-replication | rRNA genes | rrn 4.5 * | rrn5 * | rrn16 * | rrn23 * |
tRNA genes | trnA-UGC * | trnC-ACA | trnD-GUC | trnE-UUC | |
trnF-GAA | trnfM-CAU | 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-GGU | trnT-UGU | trnV-GAC * | trnV-UAC | ||
trnW-CCA | trnY-GUA | ||||
Small subunit of ribosome | rps2 | rps3 | rps4 | rps7 * | |
rps8 | rps11 | rps12 * | rps14 | ||
rps15 | rps16 | rps18 | rps19 | ||
Large subunit of ribosome | rpl2 * | rpl14 | rpl16 | rpl20 | |
rpl23 * | rpl32 | rpl33 | rpl36 | ||
RNA polymerase subunits | rpoA | rpoB | rpoC1 | rpoC2 | |
Photosynthesis | ATP synthase gene | atpA | atpB | atpE | atpF |
atpH | atpI | ||||
NADH dehydrogenase | ndhA | ndhB * | ndhC | ndhD | |
ndhE | ndhF | ndhG | ndhH | ||
ndhI | ndhJ | ndhK | |||
Cytochrome b/f complex | petA | petB | petD | petG | |
petL | petN | ||||
Photosystem I | psaA | psaB | psaC | psaI | |
psaJ | |||||
Photosystem II | psbA | psbB | psbC | psbD | |
psbE | psbF | psbH | psbI | ||
psbJ | psbK | psbL | psbM | ||
psbN | psbT | psbZ | |||
Large chain of Rubisco | rbcL | ||||
Other genes | ATP-dependent protease | clpP | |||
Cytochrome c biogenesis | ccsA | ||||
Acetyl-CoA carboxylase | accD | ||||
Translation initiation factor IF-1 | infA | ||||
Membrane protein | cemA | ||||
Maturase | matK | ||||
Unknown function | Hypothetical chloroplast reading frame | ycf1 | ycf2 * | ycf3 | ycf4 |
ycf15 * |
Gene | Location | Exon I (bp) | Intron I (bp) | Exon II (bp) | Intron II (bp) | Extron III (bp) |
---|---|---|---|---|---|---|
trnK-UUU | LSC | 35 | 2490 | 37 | ||
rps16 | LSC | 217 | 825 | 44 | ||
trnG-UCC | LSC | 24 | 768 | 48 | ||
atpF | LSC | 411 | 706 | 144 | ||
rpoC1 | LSC | 1624 | 722 | 434 | ||
ycf3 | LSC | 154 | 729 | 227 | 739 | 126 |
trnL-UAA | LSC | 35 | 491 | 50 | ||
trnV-UAC | LSC | 37 | 584 | 56 | 565 | 39 |
clpP | LSC | 246 | 630 | 291 | 781 | 69 |
petB | LSC | 5 | 786 | 641 | ||
rpl2 | IR | 432 | 658 | 387 | ||
rps12 | IR/LSC | 114 | - | 25 | 536 | 232 |
ndhB | IR | 756 | 700 | 777 | ||
trnI-GAU | IR | 42 | 936 | 35 | ||
trnA-UGC | IR | 38 | 799 | 35 | ||
ndhA | SSC | 541 | 1078 | 551 |
Codon | Amino Acid | Count | RSCU | Codon | Amino Acid | Count | RSCU |
---|---|---|---|---|---|---|---|
UUU | Phe | 714 | 1.1 | UAU | Tyr | 600 | 1.47 |
UUC | Phe | 586 | 0.9 | UAC | Tyr | 214 | 0.53 |
UUA | Leu | 671 | 1.66 | UAA | * | 147 | 0.98 |
UUG | Leu | 510 | 1.26 | UAG | * | 137 | 0.91 |
CUU | Leu | 439 | 1.09 | CAU | His | 429 | 1.41 |
CUC | Leu | 206 | 0.51 | CAC | His | 178 | 0.59 |
CUA | Leu | 400 | 0.99 | CAA | Gln | 560 | 1.41 |
CUG | Leu | 197 | 0.49 | CAG | Gln | 237 | 0.59 |
AUU | Ile | 893 | 1.28 | AAU | Asn | 712 | 1.44 |
AUC | Ile | 545 | 0.78 | AAC | Asn | 278 | 0.56 |
AUA | Ile | 647 | 0.93 | AAA | Lys | 777 | 1.37 |
AUG | Met | 602 | 1 | AAG | Lys | 359 | 0.63 |
GUU | Val | 474 | 1.37 | GAU | Asp | 631 | 1.54 |
GUC | Val | 202 | 0.58 | GAC | Asp | 189 | 0.46 |
GUA | Val | 487 | 1.41 | GAA | Glu | 780 | 1.42 |
GUG | Val | 223 | 0.64 | GAG | Glu | 318 | 0.58 |
UCU | Ser | 457 | 1.6 | UGU | Cys | 214 | 1.36 |
UCC | Ser | 266 | 0.93 | UGC | Cys | 100 | 0.64 |
UCA | Ser | 373 | 1.3 | UGA | * | 166 | 1.11 |
UCG | Ser | 192 | 0.67 | UGG | Trp | 427 | 1 |
CCU | Pro | 345 | 1.41 | CGU | Arg | 256 | 1.15 |
CCC | Pro | 213 | 0.87 | CGC | Arg | 72 | 0.32 |
CCA | Pro | 307 | 1.25 | CGA | Arg | 289 | 1.3 |
CCG | Pro | 117 | 0.48 | CGG | Arg | 129 | 0.58 |
ACU | Thr | 426 | 1.49 | AGU | Ser | 324 | 1.13 |
ACC | Thr | 237 | 0.83 | AGC | Ser | 107 | 0.37 |
ACA | Thr | 358 | 1.26 | AGA | Arg | 410 | 1.84 |
ACG | Thr | 120 | 0.42 | AGG | Arg | 179 | 0.8 |
GCU | Ala | 537 | 1.82 | GGU | Gly | 542 | 1.33 |
GCC | Ala | 185 | 0.63 | GGC | Gly | 171 | 0.42 |
GCA | Ala | 335 | 1.13 | GGA | Gly | 628 | 1.54 |
GCG | Ala | 126 | 0.43 | GGG | Gly | 291 | 0.71 |
Species | Number | Location | Regions | ||||
---|---|---|---|---|---|---|---|
LSC | IR | SSC | CDS | Intron | IGS | ||
M. cathcartii | 143 | 103 | 7 | 26 | 25 | 18 | 100 |
M. insignis | 141 | 102 | 7 | 25 | 26 | 15 | 100 |
M. laevifolia | 141 | 101 | 7 | 26 | 27 | 18 | 96 |
M. odora | 138 | 99 | 7 | 25 | 24 | 19 | 95 |
M. shiluensis | 141 | 102 | 7 | 25 | 25 | 19 | 97 |
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Deng, Y.; Luo, Y.; He, Y.; Qin, X.; Li, C.; Deng, X. Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species. Forests 2020, 11, 267. https://doi.org/10.3390/f11030267
Deng Y, Luo Y, He Y, Qin X, Li C, Deng X. Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species. Forests. 2020; 11(3):267. https://doi.org/10.3390/f11030267
Chicago/Turabian StyleDeng, Yanwen, Yiyang Luo, Yu He, Xinsheng Qin, Chonggao Li, and Xiaomei Deng. 2020. "Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species" Forests 11, no. 3: 267. https://doi.org/10.3390/f11030267
APA StyleDeng, Y., Luo, Y., He, Y., Qin, X., Li, C., & Deng, X. (2020). Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species. Forests, 11(3), 267. https://doi.org/10.3390/f11030267