Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, DNA Extraction, and Sequencing
2.2. CpDNA Assembly and Annotation
2.3. Codon Preference Analysis and Repeat Sequence Analysis
2.4. Comparative Genomics Analysis of the Chloroplast Genome
2.5. Phylogenetic Analysis
3. Results
3.1. Analysis of Characteristics of Chloroplast Genomes
3.2. Codon Usage Bias
3.3. Repeat Sequences and SSR Analysis
3.4. Comparative Genome Analysis
3.5. Phylogenetic Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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No. | Species | From | GenBank Accession No. |
---|---|---|---|
1 | Stephania japonica var. timoriensis | This study | PP175340 |
2 | Stephania japonica var. discolor | This study | PP175339 |
3 | Stephania cephalantha | GenBank | NC_067079 |
4 | Stephania dielsiana | GenBank | NC_054337 |
5 | Stephania epigaea | GenBank | NC_058988 |
6 | Stephania japonica | GenBank | NC_029432 |
7 | Stephania kwangsiensis | GenBank | NC_048524 |
8 | Stephania tetrandra | GenBank | NC_050924 |
9 | Pericampylus glaucus | GenBank | NC_046846 |
10 | Menispermum canadense | GenBank | NC_048451 |
11 | Menispermum dauricum | GenBank | NC_042371 |
12 | Sinomenium acutum | GenBank | MT040976 |
13 | Fibraurea recisa | GenBank | NC_060536 |
14 | Akebia quinata | GenBank | KX611091 |
15 | Decaisnea insignis | GenBank | KY200671 |
16 | Thalictrum baicalense | GenBank | MW133265 |
17 | Thalictrum minus | GenBank | NC_041544 |
18 | Berberis amurensis | GenBank | KM057374 |
19 | Nandina domestica | GenBank | DQ923117 |
20 | Sinopodophyllum hexandrum | GenBank | KR779994 |
21 | Epimedium lishihchenii | GenBank | KU522472 |
22 | Vancouveria planipetala | GenBank | MH337373 |
Species | Genome | LSC | IR | SSC | ||||
---|---|---|---|---|---|---|---|---|
Length/bp | GC/% | Length/bp | GC/% | Length/bp | GC/% | Length/bp | GC/% | |
S. japonica var. timoriensis | 157,609 | 38.25 | 88,477 | 36.46 | 24,393 | 43.72 | 20,346 | 32.94 |
S. japonica var. discolor | 157,748 | 38.26 | 88,581 | 36.46 | 24,401 | 43.73 | 20,365 | 32.97 |
Gene Function | Gene Group | Gene Name | Number |
---|---|---|---|
Gene for photosynthesis | 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 | |
NADH dehydrogenase | ndhA, ndhB a, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | 6 | |
Rubisco large subunits | rbcL | 1 | |
Self-replication | Lange subunits of ribosome | rpl2 a, rpl14, rpl16, rpl20, rpl22, rpl23 a, rpl32, rpl33, rpl36 | 11 |
Small subunits of ribosome | rps2, rps3, rps4, rps7 a, rps8, rps11, rps12 a, rps14, rps15, rps16, rps18, rps19 | 14 | |
RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | 4 | |
Ribosomal RNA genes | rrn4.5S a, rrn5S a, rrn16S a, rrn23S a | 8 | |
Transfer RNA genes | trnA-UGC a, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU a, trnI-GAU a, trnK-UUU, trnL-CAA a, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU a, trnP-UGG, trnQ-UUG, trnR-ACG a, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC a, trnV-UAC, trnW-CCA, trnY-GUA | 37 | |
Other genes | Protease | clpP | 1 |
Maturase | matK | 1 | |
Translation initiation factor | infA | 1 | |
Envelop membrane protein | cemA | 1 | |
Subunits of acety-CoA-carboxylase | accD | 1 | |
C-type cytochrome synthesis | ccsA | 1 | |
Unknow gene | Hypothetical chloroplast reading frames | ycf1, ycf2 a, ycf3, ycf4 | 5 |
Total | 130 |
Types and Regions | Name | S. japonica var. timoriensis | S. japonica var. discolor |
---|---|---|---|
Types | mononucleotide | 168 | 176 |
dinucleotide | 18 | 18 | |
trinucleotide | 7 | 6 | |
tetranucleotide | 9 | 7 | |
pentanucleotide | 5 | 4 | |
Regions | LSC | 142 | 143 |
SSC | 45 | 48 | |
IR | 20 | 20 | |
Total | 207 | 211 |
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Wu, L.-L.; Geng, Y.-M.; Zheng, L.-P. Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor. Genes 2024, 15, 877. https://doi.org/10.3390/genes15070877
Wu L-L, Geng Y-M, Zheng L-P. Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor. Genes. 2024; 15(7):877. https://doi.org/10.3390/genes15070877
Chicago/Turabian StyleWu, Li-Li, Ying-Min Geng, and Lan-Ping Zheng. 2024. "Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor" Genes 15, no. 7: 877. https://doi.org/10.3390/genes15070877