Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. DNA Extraction and Genome Sequencing
2.3. Chloroplast Genome Assembly and Annotation
2.4. Repeat Sequence and Codon Usage Analysis
2.5. Genome Comparison and Sequence Divergence
2.6. Phylogenetic Research
3. Results and Discussion
3.1. Genome Features
3.2. Codon Usage and Repeat Sequence Analysis
3.3. Genome Comparison
3.4. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Collecting Number | Longitude | Latitude | Altitude | Province | Herbaria |
---|---|---|---|---|---|---|
Salix spathulifolia | HLCS19_15 | 108.80° E | 33.86° N | 2456 m | Shaanxi | BJFC |
Salix cupularis | HLCS19_45 | 107.81° E | 34.00° N | 3377 m | Shaanxi | BJFC |
Salix annulifera | ZZX2019091207 | 94.97° E | 29.47° N | 3559 m | Tibet | BJFC |
S. spathulifolia | S. cupularis | S. annulifera | ||
---|---|---|---|---|
Accession Number | HLCS19_15 | HLCS19_45 | ZZX2019091207 | |
Genome | Length (bp) | 155,680 | 155,566 | 155,626 |
GC (%) | 36.7 | 36.7 | 36.7 | |
LSC | Length (bp) | 84,552 | 84,431 | 84,499 |
GC (%) | 34.4 | 34.4 | 34.4 | |
Length (%) | 54.31 | 54.27 | 54.30 | |
SSC | Length (bp) | 16,206 | 16,217 | 16,221 |
GC (%) | 31.0 | 31.0 | 30.9 | |
Length (%) | 10.41 | 10.42 | 10.42 | |
IR | Length (bp) | 27,461 | 27,459 | 27,453 |
GC (%) | 41.9 | 41.9 | 41.9 | |
Length (%) | 17.64 | 17.65 | 17.64 | |
No. of genes (duplicated in IR) | Genes | 130 (19) | 130 (20) | 130 (21) |
PCGs | 85 (8) | 85 (9) | 85 (10) | |
tRNA | 37 (7) | 37 (8) | 37 (9) | |
rRNA | 8 (4) | 8 (5) | 8 (6) | |
With introns | 17 (5) | 17 (6) | 17 (7) |
Groups of Genes | Name of Genes |
---|---|
Transfer RNAs | trnA-UGC *, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU *, trnI-GAU *, trnK-UUU, trnL-CAA *, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU *, trnP-UGG, trnQ-UUG, trnR-ACG *, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC *, trnV-UAC, trnW-CCA, trnY-GUA |
Ribosomal RNAs | rrn4.5 *, rrn5 *, rrn16 *, rrn23 * |
Ribosomal protein small subunit | rps2, rps3, rps4, rps7 *, rps8, rps11, rps12 *, rps14, rps15, rps18, rps19 * |
Ribosomal protein large subunit | rpl2 *, rpl14, rpl16, rpl20, rpl22, rpl23 *, rpl33, rpl36 |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 |
Photosystem I | psaA, psaB, psaC, psaI, psaJ, ycf3, ycf4 |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ |
Cytochrome b/f complex | petA, petB, petD, petG, petL, petN |
ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI |
NDH complex | ndhA, ndhB *, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
Large subunit Rubisco | rbcL |
Acetyl-CoA carboxylase | accD |
Maturase | matK |
Inner membrane protein | cemA |
ATP-dependent protease | clpP |
Cytochrome c biogenesis | ccsA |
Conserved open reading frames | ycf1, ycf2 *, ycf15 * |
Gene | Location | Exon I (bp) | Intron I (bp) | Exon II (bp) | Intron II (bp) | Extron III (bp) |
---|---|---|---|---|---|---|
trnK-UUU | LSC | 37 | 2547 | 35 | ||
rpl16 | LSC | 9 | 1120 | 399 | ||
trnG-UCC | LSC | 23 | 693 | 48 | ||
atpF | LSC | 145 | 741 | 398 | ||
rpoC1 | LSC | 453 | 777 | 1617 | ||
ycf3 | LSC | 126 | 723 | 228 | 667 | 153 |
trnL-UAA | LSC | 35 | 586 | 50 | ||
trnV-UAC | LSC | 39 | 609 | 35 | ||
clpP | LSC | 71 | 837 | 292 | 585 | 228 |
petB | LSC | 6 | 811 | 642 | ||
petD | LSC | 8 | 788 | 490 | ||
ndhA | SSC | 552 | 1107 | 546 | ||
rpl2 | IR | 397 | 668 | 434 | ||
rps12 | LSC&IR | 114 | ~ | 232 | 536 | 26 |
ndhB | IR | 723 | 682 | 756 | ||
trnI-GAU | IR | 37 | 949 | 35 | ||
trnA-UGC | IR | 38 | 802 | 35 |
Codon | Amino Acid | S. spathulifolia | S. cupularis | S. annulifera | |||
---|---|---|---|---|---|---|---|
Count | RSCU | Count | RSCU | Count | RSCU | ||
UUU | Phe | 987 | 1.31 | 988 | 1.31 | 992 | 1.31 |
UUC | Phe | 516 | 0.69 | 517 | 0.69 | 517 | 0.69 |
UUA | Leu | 892 | 1.91 | 894 | 1.91 | 894 | 1.91 |
UUG | Leu | 569 | 1.22 | 570 | 1.22 | 570 | 1.22 |
CUU | Leu | 586 | 1.25 | 586 | 1.25 | 586 | 1.25 |
CUC | Leu | 178 | 0.38 | 180 | 0.38 | 179 | 0.38 |
CUA | Leu | 398 | 0.85 | 397 | 0.85 | 397 | 0.85 |
CUG | Leu | 179 | 0.38 | 179 | 0.38 | 180 | 0.38 |
AUU | Ile | 1127 | 1.49 | 1129 | 1.49 | 1130 | 1.49 |
AUC | Ile | 432 | 0.57 | 432 | 0.57 | 430 | 0.57 |
AUA | Ile | 708 | 0.94 | 708 | 0.94 | 711 | 0.94 |
AUG | Met | 620 | 1 | 621 | 1 | 621 | 1 |
GUU | Val | 493 | 1.42 | 492 | 1.42 | 491 | 1.41 |
GUC | Val | 167 | 0.48 | 167 | 0.48 | 167 | 0.48 |
GUA | Val | 532 | 1.53 | 532 | 1.53 | 533 | 1.53 |
GUG | Val | 199 | 0.57 | 199 | 0.57 | 199 | 0.57 |
UCU | Ser | 572 | 1.69 | 573 | 1.69 | 573 | 1.69 |
UCC | Ser | 332 | 0.98 | 329 | 0.97 | 329 | 0.97 |
UCA | Ser | 409 | 1.21 | 408 | 1.2 | 409 | 1.21 |
UCG | Ser | 184 | 0.54 | 186 | 0.55 | 185 | 0.55 |
CCU | Pro | 418 | 1.56 | 418 | 1.57 | 420 | 1.57 |
CCC | Pro | 198 | 0.74 | 197 | 0.74 | 199 | 0.74 |
CCA | Pro | 308 | 1.15 | 306 | 1.15 | 308 | 1.15 |
CCG | Pro | 145 | 0.54 | 145 | 0.54 | 143 | 0.53 |
ACU | Thr | 522 | 1.6 | 524 | 1.6 | 524 | 1.6 |
ACC | Thr | 238 | 0.73 | 236 | 0.72 | 238 | 0.73 |
ACA | Thr | 423 | 1.29 | 424 | 1.29 | 423 | 1.29 |
ACG | Thr | 126 | 0.39 | 126 | 0.38 | 124 | 0.38 |
GCU | Ala | 620 | 1.83 | 620 | 1.83 | 620 | 1.83 |
GCC | Ala | 202 | 0.6 | 205 | 0.61 | 204 | 0.6 |
GCA | Ala | 385 | 1.14 | 385 | 1.14 | 385 | 1.14 |
GCG | Ala | 145 | 0.43 | 143 | 0.42 | 145 | 0.43 |
UAU | Tyr | 777 | 1.64 | 780 | 1.65 | 780 | 1.64 |
UAC | Tyr | 171 | 0.36 | 168 | 0.35 | 170 | 0.36 |
UAA | * | 45 | 1.59 | 45 | 1.59 | 45 | 1.59 |
UAG | * | 22 | 0.78 | 22 | 0.78 | 22 | 0.78 |
CAU | His | 477 | 1.52 | 478 | 1.52 | 477 | 1.52 |
CAC | His | 150 | 0.48 | 150 | 0.48 | 149 | 0.48 |
CAA | Gln | 713 | 1.55 | 715 | 1.55 | 716 | 1.55 |
CAG | Gln | 209 | 0.45 | 209 | 0.45 | 209 | 0.45 |
AAU | Asn | 978 | 1.53 | 981 | 1.53 | 981 | 1.53 |
AAC | Asn | 300 | 0.47 | 300 | 0.47 | 299 | 0.47 |
AAA | Lys | 1051 | 1.47 | 1052 | 1.47 | 1050 | 1.47 |
AAG | Lys | 376 | 0.53 | 376 | 0.53 | 375 | 0.53 |
GAU | Asp | 833 | 1.58 | 832 | 1.58 | 834 | 1.58 |
GAC | Asp | 223 | 0.42 | 223 | 0.42 | 222 | 0.42 |
GAA | Glu | 1023 | 1.49 | 1022 | 1.49 | 1023 | 1.49 |
GAG | Glu | 347 | 0.51 | 347 | 0.51 | 346 | 0.51 |
UGU | Cys | 213 | 1.42 | 212 | 1.42 | 213 | 1.42 |
UGC | Cys | 86 | 0.58 | 87 | 0.58 | 86 | 0.58 |
UGA | * | 18 | 0.64 | 18 | 0.64 | 18 | 0.64 |
UGG | Trp | 452 | 1 | 452 | 1 | 453 | 1 |
CGU | Arg | 328 | 1.28 | 330 | 1.29 | 330 | 1.29 |
CGC | Arg | 109 | 0.43 | 108 | 0.42 | 109 | 0.43 |
CGA | Arg | 357 | 1.4 | 361 | 1.41 | 358 | 1.4 |
CGG | Arg | 106 | 0.42 | 104 | 0.41 | 105 | 0.41 |
AGU | Ser | 408 | 1.2 | 408 | 1.2 | 407 | 1.2 |
AGC | Ser | 128 | 0.38 | 128 | 0.38 | 128 | 0.38 |
AGA | Arg | 471 | 1.84 | 471 | 1.84 | 473 | 1.85 |
AGG | Arg | 161 | 0.63 | 161 | 0.63 | 161 | 0.63 |
GGU | Gly | 556 | 1.25 | 556 | 1.25 | 557 | 1.26 |
GGC | Gly | 192 | 0.43 | 192 | 0.43 | 192 | 0.43 |
GGA | Gly | 711 | 1.6 | 711 | 1.6 | 709 | 1.6 |
GGG | Gly | 314 | 0.71 | 316 | 0.71 | 315 | 0.71 |
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Zhang, X.-J.; Liu, K.-J.; Wang, Y.-C.; He, J.; Wu, Y.-M.; Zhang, Z.-X. Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis. Forests 2021, 12, 1681. https://doi.org/10.3390/f12121681
Zhang X-J, Liu K-J, Wang Y-C, He J, Wu Y-M, Zhang Z-X. Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis. Forests. 2021; 12(12):1681. https://doi.org/10.3390/f12121681
Chicago/Turabian StyleZhang, Xue-Jiao, Kang-Jia Liu, Ya-Chao Wang, Jian He, Yuan-Mi Wu, and Zhi-Xiang Zhang. 2021. "Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis" Forests 12, no. 12: 1681. https://doi.org/10.3390/f12121681