Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of Plant Material
2.2. Physiological Indicators of the Leaves from Three Varieties
2.3. DNA Extraction and Genome Sequencing
2.4. Genome Sequence Assembly and Annotation
2.5. Chloroplast Genome Data
2.5.1. SSR and IRS Analysis
2.5.2. KaKs Calculation and Nucleotide Diversity Analysis
2.5.3. IR Boundary Analysis
2.6. Comparative Analysis of cpDNA Genomes and Related Species
2.6.1. Comparative Analysis on the Structure of Chloroplast Related Species and Chloroplast Sequence Homology Analysis
2.6.2. Genetic Distance and Phylogenetic Analysis
3. Results
3.1. Comparison of Morphology and Nutrition in Different Varieties of B. schreberi
3.2. Chloroplast Genome of ‘Mahu Chuncai’
3.3. Codon Usage Pattern Analysis
3.4. Analysis of Repeat Sequences
3.5. KaKs Analysis
3.6. Analysis of Nucleotide Diversity (Pi)
3.7. Contraction and Expansion of IR Regions
3.8. Genome Comparison and Collinearity Analysis
3.9. Phylogenetic Relationships
4. Discussion
4.1. Analysis of the Chloroplast Genome of B. schreberi
4.2. Evolutionary and Phylogenetic Relatedness
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Category | Gene Group | Gene Name |
---|---|---|
Photosynthesis | Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Subunits of NADH dehydrogenase | NdhA *, ndhB *(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Subunits of cytochrome b/f complex | petA, petB *, petD *, petG, petL, petN | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF *, atpH, atpI | |
Large subunit of rubisco | rbcL | |
Subunits photochlorophyllide reductase | - | |
Self-replication | Proteins of large ribosomal subunit | rpl14, rpl16 *, rpl2 *(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36 |
Proteins of small ribosomal subunit | rps11, rps12 **(2), rps14, rps15, rps16 *, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8 | |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1 *, rpoC2 | |
Ribosomal RNAs | rrn16(2), rrn23(2), rrn4.5(2), rrn5(2) | |
Transfer RNAs | trnA-UGC *(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC *, trnG-UCC, trnH-GUG, trnI-CAU(2), trnI-GAU *(2), trnK-UUU *, trnL-CAA(2), trnL-UAA *, trnL-UAG, trnM-CAU(2), trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC *, trnW-CCA, trnY-GUA | |
Other genes | Maturase | matK |
Protease | clpP ** | |
Envelope membrane protein | cemA | |
Acetyl-CoA carboxylase | accD | |
c-type cytochrome synthesis gene | ccsA | |
Translation initiation factor | infA | |
other | - | |
Genes of unknown function | Conserved hypothetical chloroplast ORF | orf42(2), ycf1(2), ycf2(2), ycf3 **, ycf4 |
Groups | Each Gene | All Genes | ||||
---|---|---|---|---|---|---|
KaKs > 1 | KaKs = 1 | KaKs < 1 | Ka | Ks | KaKs | |
‘Mahu Chuncai’ vs KT705316.2 | 0 | 0 | 1 | 0.01417 | 0.02794 | 0.51 |
‘Mahu Chuncai’ vs KT705317.3 | 1 | 0 | 66 | 1.03607 | 4.31501 | 0.24 |
‘Mahu Chuncai’ vs KY392763.1 | 0 | 0 | 0 | 0 | 0 | 0 |
‘Mahu Chuncai’ vs MG720559.1 | 1 | 0 | 62 | 0.99297 | 4.34761 | 0.23 |
‘Mahu Chuncai’ vs MG967470.1 | 1 | 0 | 65 | 1.03967 | 4.50068 | 0.23 |
‘Mahu Chuncai’ vs MN315507.1 | 0 | 0 | 1 | 0.89994 | 2.34814 | 0.38 |
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Sun, Y.; Li, M.; Ma, J.; He, M.; Zheng, Y. Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships. Agronomy 2022, 12, 2972. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122972
Sun Y, Li M, Ma J, He M, Zheng Y. Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships. Agronomy. 2022; 12(12):2972. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122972
Chicago/Turabian StyleSun, Yue, Mengyao Li, Junying Ma, Maolin He, and Yangxia Zheng. 2022. "Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships" Agronomy 12, no. 12: 2972. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122972