Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion
Abstract
:1. Introduction
2. Results and Discussion
2.1. Genome Organization and Comparison with Other Species
2.2. Gene Contents
2.3. Structural and Gene Rearrangements
2.4. Microsatellite Polymorphisms
2.5. Loss of ndh Genes
2.6. Contraction and Expansion of Short IRs in Pinus
2.7. Phylogenetic Analysis
3. Materials and Methods
3.1. DNA Source, Template Amplification
3.2. Sequencing, Assembly, PCR-Based Gap Filling and Annotation
3.3. Simple Sequence Repeat Analysis
3.4. Sequence Analysis
3.5. Phylogenetic Analysis
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample Availability: Sequence data of Pinus massoniana are not available from the authors. |
Category | Gene Contents |
---|---|
Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ, psaMa |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ |
Small subunit of ribosome | rps2, rps3, rps4, rps7, rps8, rps11, rps12b, rps14, rps15, rps18, rps19 |
Large subunit of ribosome | rpl2b, rpl14, rpl16b, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 |
Subunits of cytochrome b/f complex | petA, petBb, petDb, petG, petL, petN |
Subunits of ATP synthase | atpA, atpB, atpE, atpFb, atpH, atpI |
DNA-dependent RNA polymerase | rpoA, rpoB, rpoC1b, rpoC2 |
ChlorophyII biosynthesis | chlB, chlL, chlN |
Protease | clpP |
Maturase | matK |
Envelope membrane protein | cemA |
Translation initiation factor | infA |
Cytochrome c biogenesis | ccsA |
Subunit Acetyl-CoA-Carboxylate | accD |
Subunit of rubisco | rbcL |
Ribosomal RNAs | rrn4.5, rrn5, rrn16, rrn23 |
Conserved open reading frames | ycf1, ycf2, ycf3b, ycf4, ycf12, ycf68 |
Transfer RNA | trnA-UGCb, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-UCC, trnG-GCCb, trnH-GUGa, trnI-GAUab, trnK-UUUb |
trnL-CAA, trnL-UAAb, trnL-UAG, trnM-CAU, trnN-GUU, trnP-GGG, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-CCG, trnR-UCU | |
trnS-GCUa, trnS-GGA, trnS-UGA, trnT-GGUa, trnT-UGU, trnV-GAC, trnV-UACb, trnW-CCA, trnY-GUA |
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Ni, Z.; Ye, Y.; Bai, T.; Xu, M.; Xu, L.-A. Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion. Molecules 2017, 22, 1528. https://doi.org/10.3390/molecules22091528
Ni Z, Ye Y, Bai T, Xu M, Xu L-A. Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion. Molecules. 2017; 22(9):1528. https://doi.org/10.3390/molecules22091528
Chicago/Turabian StyleNi, ZhouXian, YouJu Ye, Tiandao Bai, Meng Xu, and Li-An Xu. 2017. "Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion" Molecules 22, no. 9: 1528. https://doi.org/10.3390/molecules22091528