Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill
Abstract
:1. Introduction
2. Results
2.1. CP Genome Organization and Gene Content
2.2. Repeat Structure and Simple Sequence Repeat (SSR) Analysis
2.3. Comparative Chloroplast Genomic Analysis
2.4. IR Contraction and Expansion in the L. chinense. CP Genome.
2.5. Codon Usage and RNA Editing Sites
2.6. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Material and DNA Extraction
4.2. Chloroplast Genome Sequencing and Assembly
4.3. Gene Annotation and Genome Structure
4.4. Genome Comparison and Phylogenetic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Region | Positions | T/U (%) | C (%) | A (%) | G (%) | Total (bp) |
---|---|---|---|---|---|---|
LSC | 32.7 | 18.3 | 31.4 | 17.5 | 86,595 | |
IRB | 28.4 | 20.7 | 28.5 | 22.4 | 25,476 | |
SSC | 33.9 | 16.8 | 33.7 | 15.5 | 18,209 | |
IRA | 28.5 | 22.4 | 28.4 | 20.7 | 25,476 | |
Total | 31.5 | 19.2 | 30.7 | 18.6 | 155,756 | |
CDS | 31.3 | 17.9 | 30.5 | 20.3 | 79,700 | |
1st position | 25.0 | 18.6 | 30.9 | 25.3 | 26,567 | |
2nd position | 34.0 | 19.6 | 28.5 | 18.3 | 26,567 | |
3rd position | 35.0 | 15.5 | 32.7 | 17.6 | 26,566 |
Classification of Genes | Gene Names | Number |
---|---|---|
Photosystem I | psaA, psaB, psaC, psaI, psaJ | 5 |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 |
Cytochrome b/f complex | petA, petB *, petD *, petG, petL, petN | 6 |
ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | 6 |
NADH dehydrogenase | ndhA *, ndhB * (×2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 (1) |
RubisCO large subunit | rbcL | 1 |
RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | 4 |
Ribosomal proteins (SSC) | rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps12 ** (×2), rps14, rps15, rps16 *, rps18, rps19 | 14 (2) |
Ribosomal proteins (LSC) | rpl2 (×2), rpl14, rpl16, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl36 | 11 |
Ribosomal RNAs | rrn 4.5 (×2), rrn 5 (×2), rrn 16 (×2), rrn 23 (×2) | 8 (4) |
Protein of unkown function | ycf1 (×2), ycf2 (×2), ycf3 **, ycf4 | 6 (2) |
Transfer RNAs | 37 tRNAs (8 contain an intron, 7 in the inverted repeats region) | 37 (7) |
Other genes | accD, ccsA, cemA, clpP, matK | 5 |
Total | 130 |
Gene | Location | Exon I (bp) | Intron I (bp) | Exon II (bp) | Intron II (bp) | Exon III (bp) |
---|---|---|---|---|---|---|
atpF | LSC | 410 | 704 | 145 | ||
clpP | LSC | 228 | 640 | 292 | 808 | 71 |
ndhA | SSC | 539 | 1154 | 553 | ||
ndhB | IR | 777 | 679 | 756 | ||
petB | LSC | 6 | 750 | 642 | ||
petD | LSC | 8 | 742 | 475 | ||
rpl16 | LSC | 396 | 1016 | 9 | ||
rpl2 | IR | 434 | 666 | 391 | ||
rpoC1 | LSC | 1616 | 737 | 430 | ||
rps12 | IR | 26 | 536 | 232 | ||
rps16 | LSC | 227 | 822 | 40 | ||
trnA-UGC | IR | 38 | 681 | 35 | ||
trnI-GAU | IR | 34 | 717 | 37 | ||
trnK-UUU | LSC | 36 | 2513 | 37 | ||
trnL-UAA | LSC | 35 | 497 | 50 | ||
trnV-UAC | LSC | 35 | 565 | 38 | ||
ycf3 | LSC | 154 | 756 | 229 | 744 | 124 |
SSR Type | Repeat Unit | Amount | Ratio (%) |
---|---|---|---|
Mono | A/T | 106 | 99.1 |
C/G | 1 | 0.9 | |
Di | AC/GT | 1 | 2.2 |
AG/CT | 16 | 34.8 | |
AT/TA | 29 | 63.0 | |
Tri | AAC/GTT | 9 | 13.4 |
AAG/CTT | 20 | 30.0 | |
AAT/ATT | 21 | 31.3 | |
ACC/GGT | 1 | 1.4 | |
ACG/CGT | 1 | 1.4 | |
ACT/AGT | 2 | 3.0 | |
AGC/CTG | 5 | 7.5 | |
AGG/CCT | 4 | 6.0 | |
ATC/ATG | 4 | 6.0 | |
Tetra | AAAC/GTTT | 3 | 27.3 |
AAAG/CTTT | 1 | 9.1 | |
AAAT/ATTT | 5 | 45.4 | |
AATC/ATTG | 1 | 9.1 | |
AGAT/ATCT | 1 | 9.1 |
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Yang, Z.; Huang, Y.; An, W.; Zheng, X.; Huang, S.; Liang, L. Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. Plants 2019, 8, 87. https://doi.org/10.3390/plants8040087
Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L. Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. Plants. 2019; 8(4):87. https://doi.org/10.3390/plants8040087
Chicago/Turabian StyleYang, Zerui, Yuying Huang, Wenli An, Xiasheng Zheng, Song Huang, and Lingling Liang. 2019. "Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill" Plants 8, no. 4: 87. https://doi.org/10.3390/plants8040087