Chloroplast Genome Profiling and Phylogenetic Insights of the “Qixiadaxiangshui” Pear (Pyrus bretschneideri Rehd.1)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. DNA Extraction and Sequencing
2.3. Chloroplast Genome Assembly and Annotation
2.4. Chloroplast Genome Characterization
2.5. Comparative Analysis of Chloroplast Genomes
2.6. Phylogenetic Analysis
3. Results
3.1. Structure and Composition of the Chloroplast Genome of the “Qixiadaxiangshui” Pear
3.2. RSCU Analysis of the “Qixiadaxiangshui” Pear Genome
3.3. cpSSR Analysis of the “Qixiadaxiangshui” Pear Genome
3.4. Analysis of IR Boundary Features
3.5. Comparative Analysis of Chloroplast Genomes among Pear Germplasm
3.6. Phylogenetic Analysis of Rosaceae Plants
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Region | A (%) | C (%) | G (%) | T (%) | GC (%) | Base Size (bp) |
---|---|---|---|---|---|---|
IRa | 28.6 | 22.1 | 20.54 | 28.76 | 42.64 | 26,392 |
IRb | 28.76 | 20.54 | 22.1 | 28.6 | 42.64 | 26,392 |
LSC | 32.12 | 17.64 | 16.65 | 33.6 | 34.28 | 87,863 |
SSC | 34.77 | 15.9 | 14.5 | 34.83 | 30.4 | 19,238 |
Total | 31.3 | 18.64 | 17.93 | 32.12 | 36.58 | 159,885 |
Gene Function | Gene Category | Gene Name | Number |
---|---|---|---|
Photosynthesis | Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ | 5 |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 | |
Subunits of NADH dehydrogenase | ndhA*, ndhB*(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 | |
Subunits of cytochrome b/f complex | petA, petB*, petD*, petG, petL, petN | 6 | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF*, atpH, atpI | 6 | |
Large subunit of rubis CO | rbcL | 1 | |
Proteins of large ribosomal subunit | #rpl2*, rpl14, rpl16*, rpl2*, rpl20, rpl22, rpl23(2), rpl32, rpl33 | 10 | |
Self-replication | Proteins of small ribosomal subunit | rps11, rps12**(2), rps14, rps15, rps16*, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8 | 14 |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1*, rpoC2 | 4 | |
Ribosomal RNAs | rrn16(2), rrn23(2), rrn4.5(2), rrn5(2) | 8 | |
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, 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, trnfM-CAU | 37 | |
Maturase | matK | 1 | |
Other genes | Protease | clpP** | 1 |
Envelope membrane protein | cemA | 1 | |
Acetyl-CoA carboxylase | accD | 1 | |
c-type cytochrome synthesis gene | ccsA | 1 | |
Genes of unknown function | Conserved hypothetical chloroplast ORF | #ycf1, ycf1, ycf15(2), ycf2(2), ycf3**, ycf4 | 8 |
Amino Acid | Codon | No. | Total | RSCU | Amino Acid | Codon | No. | Total | RSCU |
---|---|---|---|---|---|---|---|---|---|
* (Ter) | UAA | 47 | 84 | 1.6785 | M (Met) | AUG | 616 | 2.9904 | |
* (Ter) | UAG | 22 | 0.7857 | M (Met) | GUG | 1 | 0.0048 | ||
* (Ter) | UGA | 15 | 0.5358 | N (Asn) | AAC | 298 | 1269 | 0.4696 | |
A (Ala) | GCA | 384 | 1384 | 1.11 | N (Asn) | AAU | 971 | 1.5304 | |
A (Ala) | GCC | 213 | 0.6156 | P (Pro) | CCA | 314 | 1068 | 1.176 | |
A (Ala) | GCG | 146 | 0.422 | P (Pro) | CCC | 197 | 0.738 | ||
A (Ala) | GCU | 641 | 1.8528 | P (Pro) | CCG | 148 | 0.5544 | ||
C (Cys) | UGC | 77 | 299 | 0.515 | P (Pro) | CCU | 409 | 1.532 | |
C (Cys) | UGU | 222 | 1.485 | Q (Gln) | CAA | 714 | 927 | 1.5404 | |
D (Asp) | GAC | 207 | 1091 | 0.3794 | Q (Gln) | CAG | 213 | 0.4596 | |
D (Asp) | GAU | 884 | 1.6206 | R (Arg) | AGA | 470 | 1569 | 1.7976 | |
E (Glu) | GAA | 1010 | 1367 | 1.4776 | R (Arg) | AGG | 174 | 0.6654 | |
E (Glu) | GAG | 357 | 0.5224 | R (Arg) | CGA | 363 | 1.3884 | ||
F (Phe) | UUC | 518 | 1483 | 0.6986 | R (Arg) | CGC | 109 | 0.417 | |
F (Phe) | UUU | 965 | 1.3014 | R (Arg) | CGG | 119 | 0.4548 | ||
G (Gly) | GGA | 701 | 1736 | 1.6152 | R (Arg) | CGU | 334 | 1.2774 | |
G (Gly) | GGC | 181 | 0.4172 | S (Ser) | AGC | 127 | 2011 | 0.3792 | |
G (Gly) | GGG | 284 | 0.6544 | S (Ser) | AGU | 401 | 1.1964 | ||
G (Gly) | GGU | 570 | 1.3132 | S (Ser) | UCA | 407 | 1.2144 | ||
H (His) | CAC | 140 | 626 | 0.4472 | S (Ser) | UCC | 324 | 0.9666 | |
H (His) | CAU | 486 | 1.5528 | S (Ser) | UCG | 190 | 0.567 | ||
I (Ile) | AUA | 709 | 2244 | 0.948 | S (Ser) | UCU | 562 | 1.677 | |
I (Ile) | AUC | 433 | 0.579 | T (Thr) | ACA | 408 | 1343 | 1.2152 | |
I (Ile) | AUU | 1102 | 1.4733 | T (Thr) | ACC | 242 | 0.7208 | ||
K (Lys) | AAA | 1029 | 1379 | 1.4924 | T (Thr) | ACG | 148 | 0.4408 | |
K (Lys) | AAG | 350 | 0.5076 | T (Thr) | ACU | 545 | 1.6232 | ||
L (Leu) | CUA | 357 | 2752 | 0.7782 | V (Val) | GUA | 539 | 1415 | 1.5236 |
L (Leu) | CUC | 181 | 0.3948 | V (Val) | GUC | 161 | 0.4552 | ||
L (Leu) | CUG | 179 | 0.39 | V (Val) | GUG | 202 | 0.5712 | ||
L (Leu) | CUU | 588 | 1.2822 | V (Val) | GUU | 513 | 1.45 | ||
L (Leu) | UUA | 884 | 1.9272 | W (Trp) | UGG | 452 | 452 | 1 | |
L (Leu) | UUG | 563 | 1.2276 | Y (Tyr) | UAC | 189 | 971 | 0.3892 | |
M (Met) | AUA | 1 | 618 | 0.0048 | Y (Tyr) | UAU | 782 | 1.6108 |
Region | Exon | Intron | Intergenic | Total |
---|---|---|---|---|
LSC | 31 | 16 | 82 | 129 |
SSC | 22 | 3 | 13 | 38 |
IR | 21 | 3 | 18 | 42 |
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Jiao, H.; Chen, Q.; Xiong, C.; Wang, H.; Ran, K.; Dong, R.; Dong, X.; Guan, Q.; Wei, S. Chloroplast Genome Profiling and Phylogenetic Insights of the “Qixiadaxiangshui” Pear (Pyrus bretschneideri Rehd.1). Horticulturae 2024, 10, 744. https://doi.org/10.3390/horticulturae10070744
Jiao H, Chen Q, Xiong C, Wang H, Ran K, Dong R, Dong X, Guan Q, Wei S. Chloroplast Genome Profiling and Phylogenetic Insights of the “Qixiadaxiangshui” Pear (Pyrus bretschneideri Rehd.1). Horticulturae. 2024; 10(7):744. https://doi.org/10.3390/horticulturae10070744
Chicago/Turabian StyleJiao, Huijun, Qiming Chen, Chi Xiong, Hongwei Wang, Kun Ran, Ran Dong, Xiaochang Dong, Qiuzhu Guan, and Shuwei Wei. 2024. "Chloroplast Genome Profiling and Phylogenetic Insights of the “Qixiadaxiangshui” Pear (Pyrus bretschneideri Rehd.1)" Horticulturae 10, no. 7: 744. https://doi.org/10.3390/horticulturae10070744