The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske
"> Figure 1
<p>Map of the <span class="html-italic">Sanionia uncinata</span> plastome. Complete plastome sequences were obtained from the de novo assembly of Illumina paired-end reads. Genes are color coded by functional group, which are located in the left box. The inner darker gray circle indicates the GC content while the lighter gray corresponds to AT content. IR, inverted repeat; LSC, large single copy region; SSC, small single copy region. Genes shown on the outside of the outer circle are transcribed clockwise and those on the inside counter clockwise. The map was made with OGDraw [<a href="#B31-ijms-19-00709" class="html-bibr">31</a>].</p> "> Figure 2
<p>Alignment of complete plastome sequences from six species. Alignment and comparison were performed using mVISTA and the percentage of identity between the plastomes was visualized in the form of an mVISTA plot. The sequence similarity of the aligned regions between <span class="html-italic">S. uncinata</span> and other five species is shown as horizontal bars indicating average percent identity between 50–100% (shown on the y-axis of graph). The x-axis represents the coordinate in the plastome. Genome regions are color-coded for protein-coding (exon), rRNA, tRNA and conserved non-coding sequences (CNS) as the guide at the bottom-left.</p> "> Figure 3
<p>Phylogenetic tree reconstruction of 23 taxa using MEGA7 based on concatenated sequences of 40 protein-coding genes in the plastome. Maximum likelihood (ML) topology is shown with the bootstrap support values (MP/ML) given at nodes. Forty protein-coding sequences were extracted from annotated plastomes found in GenBank [<a href="#B21-ijms-19-00709" class="html-bibr">21</a>] (<a href="http://www.ncbi.nlm.nih.gov" target="_blank">http://www.ncbi.nlm.nih.gov</a>) (<a href="#app1-ijms-19-00709" class="html-app">Table S2</a>). The nucleotide sequences for each gene were translated into amino acids, aligned in MEGA7 and manually adjusted. Nucleotide sequences were aligned by constraining them to the amino acid sequence alignment. Individual gene alignments were then assembled into a single dataset.</p> "> Figure 4
<p>Comparison of the large inversion in the LSC region among six bryophytes plastomes. In comparative LSC region alignment of <span class="html-italic">rpoA</span>, <span class="html-italic">petN</span> coding regions from <span class="html-italic">M. polymorpha</span>, <span class="html-italic">S. uncinata</span>, <span class="html-italic">T. ruralis</span>, <span class="html-italic">T. pellucida</span> and <span class="html-italic">P. patens</span>. The inverted-arrangement of 71 kb fragment was only detected for <span class="html-italic">P. patens</span>.</p> "> Figure 5
<p>Amino acid alignment of (<b>A</b>) nuc-<span class="html-italic">rpoA</span> and (<b>B</b>) nuc-<span class="html-italic">petN</span> genes of <span class="html-italic">S. uncinata</span> with the nuc-<span class="html-italic">rpoA</span> or cp-<span class="html-italic">rpoA</span> and cp-<span class="html-italic">petN</span> genes from other green plants. Identical amino acid residues are boxed in black, other residues are printed in grey. Signal peptide sequences were predicted using SignalP [<a href="#B45-ijms-19-00709" class="html-bibr">45</a>] and shown as double arrow lines and the asterisk.</p> ">
Abstract
:1. Introduction
2. Results and Discussion
2.1. Overall Genome Organization
2.2. Comparison with Other Bryophyte Plastomes
2.3. Phylogenomic Analysis
2.4. Loss of rpoA and petN in the S. uncinata Plastome
2.5. Identification of Nuclear Genes Encoding rpoA and petN
2.6. Prediction of RNA Editing Sites of Chloroplast Genes
3. Materials and Methods
3.1. Ethics Statement
3.2. Plant Culture Conditions
3.3. Library Preparation and Sequencing
3.4. Assembly and Annotation
3.5. Genome Alignment
3.6. Phylogenetic Analysis
3.7. Prediction of RNA-Editing Sites
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
LSC | Large single copy |
SSC | Small single copy |
IR | Inverted repeat |
Cp | Chloroplast |
nuc | Nucleus |
MP | Maximum parsimony |
ML | Maximum likelihood |
A | Adenine |
T | Thymine |
G | Guanine |
C | cytosine |
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Gene Products | Genes |
---|---|
Photosystem I | psaA, B, C, I, J, M |
Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z |
Cytochrome b6/f | petA, B a, D a, G, L |
ATP synthase | atpA, B, E, F a, H, I |
Translation factor | infA |
Chlorophyll biosynthesis | chlB, L, N |
Rubisco | rbcL |
NADH oxidoreductase | ndhA a, B a, C, D, E, F, G, H, I, J, K |
Large subunit ribosomal proteins | rpl2 a, 14, 16 a, 20, 21, 22, 23, 32, 33, 36 |
Small subunit ribosomal proteins | rps2, 3, 4, 7, 8, 11, 12 a,b, 14, 15, 18, 19 |
RNAP | rpoB, C1 a, C2 |
Other proteins | accD, cemA, clpP c, matK |
Proteins of unknown function | ycf1, 2, 3 c, 4, 12, 66 a |
Ribosomal | rrn4.5 d, 5 d, 16 d, 23 d |
Transfer RNAs | trnA(UGC) a,d, C(GCA), D(GUC), E(UUC), F(GAA), G(UCC) a, G(UCC), H(GUG), I(CAU), I(GAU) a,d, K(UUU) a, L(CAA), L(UAA) a, L(UAG), fM(CAU), M(CAU), N(GUU) d, P(UGG), P(GGG), Q(UUG), R(ACG) d, R(CCG), R(UCU), S(GCU), S(GGA), S(UGA), T(GGU), T(UGU), V(GAC) d, V(UAC) a, W(CCA), Y(GUA) |
Gene | Location | Length (bp) | ||||
---|---|---|---|---|---|---|
Exon I | Intron I | Exon II | Intron II | Exon III | ||
rps12 | LSC | 114 | - | 270 | ||
ndhB | LSC | 729 | 629 | 780 | ||
ycf66 | LSC | 106 | 591 | 320 | ||
rpoC1 | LSC | 423 | 789 | 1614 | ||
atpF | LSC | 411 | 654 | 135 | ||
ycf3 | LSC | 126 | 684 | 228 | 739 | 153 |
clpP | LSC | 69 | 687 | 291 | 483 | 234 |
rpl2 | LSC | 396 | 637 | 438 | ||
ndhA | SSC | 556 | 731 | 551 | ||
trnK-UUU | LSC | 37 | 2272 | 42 | ||
trnL-UAA | LSC | 38 | 262 | 50 | ||
trnV-UAC | LSC | 37 | 542 | 37 | ||
trnI-GAU | IR | 42 | 769 | 35 | ||
trnA-UGC | IR | 38 | 763 | 35 |
Amino Acid | Codon | No. * | tRNA | Amino Acid | Codon | No. * | tRNA |
---|---|---|---|---|---|---|---|
Phe | UUU | 2862 | Tyr | UAU | 1492 | ||
Phe | UUC | 916 | trnF-GAA | Tyr | UAC | 578 | trnY-GUA |
Leu | UUG | 688 | trnL-UAA | Stop | UAA | 1772 | |
Leu | UUA | 1766 | trnL-CAA | Stop | UAG | 577 | |
Leu | CUG | 252 | His | CAU | 550 | ||
Leu | CUA | 591 | trnL-UAG | His | CAC | 224 | trnH-GUG |
Leu | CUU | 741 | Gln | CAA | 685 | trnQ-UUG | |
Leu | CUC | 305 | Gln | CAG | 273 | ||
Ile | AUG | 1582 | trnI-CAU | Asn | AAU | 1878 | |
Ile | AUU | 1943 | Asn | AAC | 665 | trnN-GUU | |
Ile | AUC | 629 | trnI-GAU | Lys | AAA | 2942 | trnK-UUU |
Met | AUG | 515 | trnfM-CAU | Lys | AAG | 768 | |
Val | GUG | 244 | Asp | GAU | 619 | ||
Val | GUA | 588 | trnV-UAC | Asp | GAC | 210 | trnD-GUC |
Val | GUU | 652 | Glu | GAA | 845 | trnE-UUC | |
Val | GUC | 237 | trnV-GAC | Glu | GAG | 286 | |
Ser | AGU | 579 | Cys | UGU | 515 | ||
Ser | AGC | 470 | trnS-GCU | Cys | UGC | 362 | trnC-GCA |
Ser | UCG | 272 | Stop | UGA | 657 | ||
Ser | UCA | 643 | trnS-UGA | Trp | UGG | 455 | trnW-CCA |
Pro | CCG | 169 | Arg | AGG | 387 | ||
Pro | CCA | 429 | trnP-UGG | Arg | AGA | 732 | trnR-UCU |
Pro | CCU | 423 | Arg | CGG | 164 | trnR-CCG | |
Pro | CCC | 230 | trnP-GGG | Arg | CGA | 322 | |
Thr | ACG | 228 | Arg | CGU | 270 | trnR-ACG | |
Thr | ACA | 508 | trnT-UGU | Arg | CGC | 143 | |
Thr | ACU | 561 | Ser | UCU | 735 | ||
Thr | ACC | 363 | trnT-GGU | Ser | UCC | 419 | trnS-GGA |
Ala | GCG | 155 | Gly | GGG | 426 | ||
Ala | GCA | 367 | trnA-UGC | Gly | GGA | 465 | trnG-UCC |
Ala | GCU | 413 | Gly | GGU | 653 | ||
Ala | GCC | 514 | Gly | GGC | 237 |
Plants * | Genome Size (bp) | petN | rpoA | ccsA | cysA | cysT | ycf66 | matK | rps15 | trnP-GGG | |
---|---|---|---|---|---|---|---|---|---|---|---|
Alga | Chlorella vulgaris | 150,613 | - | + | + | + | + | - | - | - | - |
Hornwort | Anthoceros formosae | 161,162 | + | + | + | + | + | - | Ψ | Ψ | + |
Liverwort | Marchantia polymorpha | 121,024 | + | + | + | + | + | + | + | + | Ψ |
Moss | Tetraphis pellucida | 127,489 | - | - | - | - | - | + | + | + | - |
Moss | Physcomitrella patens | 122,890 | + | - | - | - | - | + | + | + | - |
Moss | Tortula rularis | 122,630 | - | - | - | - | - | + | + | + | + |
Moss | Sanionia uncinata | 124,374 | - | - | - | - | - | + | + | + | + |
Lycopodiophyta | Huperzia lucidula | 154,373 | + | + | + | - | - | + | + | + | + |
Moniliformopses | Equisetum arvense | 133,309 | + | + | + | - | - | + | + | + | + |
Acrogymnospermae | Pinus thunbergii | 116,635 | + | + | + | - | - | - | + | + | + |
Magnoliophyta | Arabidopsis thaliana | 154,515 | + | + | + | - | - | - | + | + | - |
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Park, M.; Park, H.; Lee, H.; Lee, B.-h.; Lee, J. The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske. Int. J. Mol. Sci. 2018, 19, 709. https://doi.org/10.3390/ijms19030709
Park M, Park H, Lee H, Lee B-h, Lee J. The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske. International Journal of Molecular Sciences. 2018; 19(3):709. https://doi.org/10.3390/ijms19030709
Chicago/Turabian StylePark, Mira, Hyun Park, Hyoungseok Lee, Byeong-ha Lee, and Jungeun Lee. 2018. "The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske" International Journal of Molecular Sciences 19, no. 3: 709. https://doi.org/10.3390/ijms19030709
APA StylePark, M., Park, H., Lee, H., Lee, B. -h., & Lee, J. (2018). The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske. International Journal of Molecular Sciences, 19(3), 709. https://doi.org/10.3390/ijms19030709