Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships
Abstract
:1. Introduction
2. Results and Discussions
2.1. Chloroplast Genome Features of M. hupehensis
2.2. SSR and Long-Repeat Analysis
2.3. IR Contraction and Expansion
2.4. Comparative Chloroplast Genomic Analysis
2.5. Phylogenetic Analysis
3. Materials and Methods
3.1. Plant Materials and DNA Sequencing
3.2. Genome Assembly and Genome Annotation
3.3. Sequence Analysis
3.4. Comparative Genome Analysis
3.5. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
cp | Chloroplast |
PCGs | Protein-coding genes |
tRNAs | Transfer RNA genes |
rRNAs | Ribosomal RNA genes |
IRs | Inverted repeat regions |
LSC | Large single copy |
SSC | Small single copy |
SSR | Simple sequence repeat |
ML | Maximum likelihood |
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Sample Availability: Samples of M. hupehensis are available from the authors. |
Genome Characteristics | M. hupehensis | M. trilobata | M. florentina | M. tschonoskii | M. baccata | M. micromalus | M. prunifolia | M. doumeri | M. yunnanensis |
---|---|---|---|---|---|---|---|---|---|
Accession number | MK020147 | KX499858 | KX499862 | KX499863 | KX499859 | MF062434 | KU851961 | KX499861 | MH394388 |
Genome size (bp) | 160,065 | 160,207 | 159,712 | 160,053 | 160,163 | 159,834 | 160,041 | 159,584 | 160,068 |
LSC length (bp) | 88,166 | 88,107 | 87,710 | 88,137 | 88,267 | 87,950 | 88,119 | 87,670 | 88,245 |
SSC length (bp) | 19,193 | 19,316 | 19,250 | 19,210 | 19,188 | 19,176 | 19,204 | 19,168 | 19,211 |
IR length (bp) | 26,353 | 26,392 | 26,376 | 26,353 | 26,354 | 26,354 | 26,359 | 26,373 | 26,306 |
No. of different genes | 112 | 110 | 110 | 110 | 109 | 111 | 111 | 110 | 112 |
No. of different protein-coding genes | 78 | 76 | 77 | 77 | 76 | 77 | 77 | 77 | 78 |
No. of different tRNA genes | 30 | 30 | 29 | 29 | 29 | 30 | 30 | 29 | 30 |
No. of different rRNA genes | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 4 |
% GC content in LSC | 34.2 | 34.2 | 34.3 | 34.2 | 34.2 | 34.3 | 34.2 | 34.4 | 34.2 |
% GC content in SSC | 30.4 | 30.3 | 30.4 | 30.4 | 30.4 | 30.4 | 30.4 | 30.4 | 30.4 |
% GC content in IR | 42.7 | 42.6 | 42.6 | 42.7 | 42.7 | 42.7 | 42.7 | 42.6 | 42.7 |
% GC content of genome | 36.6 | 36.5 | 36.6 | 36.5 | 36.5 | 36.6 | 36.6 | 36.6 | 36.5 |
Group of Genes | Gene Name |
---|---|
DNA-dependent RNA polymerase | rpoA, rpoB, rpoC1#, rpoC2 |
tRNA genes | 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, trnfM-CAU, trnM-CAU, trnN-GUU (×2), trnP-GGG, 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 |
Ribosomal small subunit | rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps12 # (×2), rps14, rps15, rps16 #, rps18, rps19 (×2) |
Ribosomal large subunit | rpl2# (×2), rpl14, rpl16 #, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl36 |
rRNA genes | rrn16 (×2), rrn23 (×2), rrn4.5 (×2), rrn5 (×2) |
ATP synthase | atpA, atpB, atpE, atpF#, atpH, atpI |
Photosystem I | psaA, psaB, psaC, psaI, psaJ |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ |
NADH dehydrogenase | ndhA#, ndhB# (×2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
Cytochrome b/f complex | petA, petB#, petD #, petG, petL, petN |
Large subunit of rubisco | rbcL |
Maturase | matK |
Subunit of acetyl-CoA carboxylase | accD |
Envelope membrane protein | cemA |
Protease | clpP## |
c-type cytochrome synthesis | ccsA |
Conserved open reading frames | ycf1 (×2), ycf2 (×2), ycf3 ##, ycf4 |
Gene | Location | ExonI (bp) | IntronI (bp) | ExonII (bp) | IntronII (bp) | ExonIII (bp) |
---|---|---|---|---|---|---|
trnK-UUU | LSC | 37 | 2497 | 35 | ||
trnG-UCC | LSC | 23 | 698 | 48 | ||
trnL-UAA | LSC | 37 | 514 | 50 | ||
trnV-UAC | LSC | 39 | 592 | 37 | ||
trnI-GAU | IR | 42 | 943 | 35 | ||
trnA-UGC | IR | 38 | 807 | 35 | ||
rps12 * | LSC | 114 | - | 232 | 541 | 26 |
rps16 | LSC | 40 | 864 | 221 | ||
rpl16 | LSC | 9 | 983 | 399 | ||
rpl2 | IR | 390 | 686 | 435 | ||
rpoC1 | LSC | 435 | 741 | 1611 | ||
ndhA | SSC | 552 | 1134 | 540 | ||
ndhB | IR | 777 | 669 | 756 | ||
ycf3 | SSC | 126 | 708 | 228 | 744 | 153 |
petB | LSC | 6 | 797 | 642 | ||
atpF | LSC | 144 | 737 | 411 | ||
clpP | LSC | 71 | 826 | 292 | 627 | 228 |
petD | LSC | 8 | 724 | 475 |
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Zhang, X.; Rong, C.; Qin, L.; Mo, C.; Fan, L.; Yan, J.; Zhang, M. Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. Molecules 2018, 23, 2917. https://doi.org/10.3390/molecules23112917
Zhang X, Rong C, Qin L, Mo C, Fan L, Yan J, Zhang M. Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. Molecules. 2018; 23(11):2917. https://doi.org/10.3390/molecules23112917
Chicago/Turabian StyleZhang, Xin, Chunxiao Rong, Ling Qin, Chuanyuan Mo, Lu Fan, Jie Yan, and Manrang Zhang. 2018. "Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships" Molecules 23, no. 11: 2917. https://doi.org/10.3390/molecules23112917