Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis
Abstract
:1. Introduction
2. Results
2.1. Features of the T. paniculatum cp Genome
2.2. Codon Usage of the T. paniculatum cp Genome
2.3. Repeats Structure and SSR in T. paniculatum cp Genome
2.4. matK and rpl23 Diversity Analysis
2.5. Comparative Analysis of the Chloroplast Genomes of the Caryophyllales
2.6. IR Expansion and Contraction
2.7. Phylogenetic Analysis
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. DNA Sequencing and Genome Assembly
5.2. Gene Annotation and Codon Usage Analysis
5.3. Repeat Structure and Single Sequence Repeats (SSRs) Analysis
5.4. Comparative Genome Analysis of the T. paniculatum with Eight cp Genomes of Caryophyllales
5.5. Phylogenetic Analysis
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample Availability: Samples of the T. paniculatum are available from the authors. |
Region | Size (bp) | T(U) (%) | C (%) | A (%) | G (%) | Genes | Protein-Coding Genes | tRNA Genes | rRNA Genes |
---|---|---|---|---|---|---|---|---|---|
LSC | 86,898 | 33.2 | 17.8 | 32.2 | 16.8 | 83 | 56 | 22 | 0 |
SSC | 18,529 | 34.6 | 15.9 | 34.9 | 14.6 | 12 | 12 | 1 | 0 |
IRA | 25,751 | 29.0 | 22.3 | 28.2 | 20.4 | 19 | 7 | 7 | 4 |
IRB | 25,751 | 28.2 | 20.4 | 29.0 | 22.3 | 19 | 8 | 7 | 4 |
Total | 156,929 | 31.8 | 19.0 | 30.7 | 18.5 | 128 | 83 (4) | 37 (7) | 8 (4) |
CDS | 78,438 | 31.5 | 17.6 | 30.8 | 20.1 | ||||
1st position | 26,146 | 23.7 | 18.8 | 30.7 | 26.7 | ||||
2nd position | 26,146 | 32.7 | 20.2 | 29.4 | 17.8 | ||||
3rd position | 26,146 | 38.1 | 13.7 | 32.4 | 15.7 |
Group of Genes | Name of Gene | No. |
---|---|---|
Photosytem I | psaA, psaB, psaC, psaI, psaJ | 5 |
Photosytem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 |
Cytochrome b/f complex | petA, petB, petD, petG, petL, petN | 6 |
ATP system | atpA, atpB, atpF, atpF, atpH, atpI | 6 |
NADH dehydrogenase | ndhA, ndhB *, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 |
RuBisCO large subnit | rbcL | 1 |
RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | 4 |
Ribosomal proteins (SSU) | rps2, rps3, rps4, rps7 *, rps8, rps11, rps12 *, rps14, rps15, rps16, rps18, rps19 | 14 |
Ribosomal proteins (LSU) | rpl2, rpl14, rpl16, rpl19, rpl20, rpl22, rpl32, rpl33, rpl36 | 9 |
Miscellaneous proteins | accD, cemA, ccsA, clpP, infA, matK | 6 |
Hypothetical chloroplast reading frames (ycf) | ycf1, ycf2 *, ycf3, ycf4 | 5 |
Transfer RNAs | trnA-UGC *, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC, trnG-GCC, trnH-GUG, trnI-CAU *, trnIGAU *, trnK-UUU, trnL-UAA, trnL-CAA *, trnL-UAG, trnM-CAU, trnN-GUU *, trnP-UGG, trnQ-UUG, trnR-UCU, trnRACG *, trnS-GCU, trnS-UGA, trnS-GGA, trnT-GGU, trnT-UGU, trnV-UAC, trnV-GAC *, trnW-CCA, trnY-GUA, trnfM-CAU | 37 |
Ribosomal RNAs | rrn4.5 *, rrn5 *, rrn16 *, rrn23 * | 8 |
Pseudogene | rpl23 *, rps19, ycf1 | 4 |
Total | 132 |
No. | Gene | Location | ExonI (bp) | IntronI (bp) | ExonII (bp) | IntronII (bp) | ExonIII (bp) |
---|---|---|---|---|---|---|---|
1 | trnK-UUU | LSC | 35 | 2502 | 37 | ||
2 | rps16 | LSC | 202 | 867 | 41 | ||
3 | trnG-UCC | LSC | 23 | 707 | 48 | ||
4 | atpF | LSC | 410 | 745 | 145 | ||
5 | rpoC1 | LSC | 1611 | 794 | 432 | ||
6 | ycf3 | LSC | 153 | 773 | 229 | 769 | 125 |
7 | trnL-UAA | LSC | 37 | 599 | 50 | ||
8 | trnV-UAC | LSC | 35 | 586 | 38 | ||
9 | clpP | LSC | 229 | 590 | 291 | 894 | 71 |
10 | petB | LSC | 6 | 768 | 642 | ||
11 | petD | LSC | 8 | 792 | 475 | ||
12 | rpl16 | LSC | 399 | 1102 | 9 | ||
13 | ndhB * | IR | 756 | 668 | 777 | ||
14 | rps12 * | IR | 114 | - | 232 | 533 | 26 |
15 | trnI-GAU * | IR | 37 | 947 | 35 | ||
16 | trnA-UGC * | IR | 38 | 818 | 35 | ||
17 | ndhA | SSC | 539 | 1087 | 553 |
Amino Acid | Codon | Count | RSCU | Amino Acid | Codon | Count | RSCU | Amino Acid | Codon | Count | RSCU | Amino Acid | Codon | Count | RSCU |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phe | UUU(F) | 975 | 1.3 | Ser | UCU(S) | 556 | 1.67 | Tyr | UAU(Y) | 779 | 1.61 | Stop | UGA(*) | 20 | 0.72 |
Phe | UUC(F) | 527 | 0.7 | Ser | UCC(S) | 331 | 0.99 | Tyr | UAC(Y) | 190 | 0.39 | Trp | UGG(W) | 460 | 1 |
Leu | UUA(L) | 854 | 1.84 | Ser | UCA(S) | 408 | 1.22 | Stop | UAA(*) | 46 | 1.66 | Ala | GCU(A) | 615 | 1.75 |
Leu | UUG(L) | 554 | 1.2 | Ser | UCG(S) | 187 | 0.56 | Stop | UAG(*) | 17 | 0.61 | Ala | GCC(A) | 234 | 0.66 |
Leu | CUU(L) | 601 | 1.3 | Ser | AGU(S) | 393 | 1.18 | His | CAU(H) | 448 | 1.49 | Ala | GCA(A) | 416 | 1.18 |
Leu | CUC(L) | 179 | 0.39 | Ser | AGC(S) | 127 | 0.38 | His | CAC(H) | 155 | 0.51 | Ala | GCG(A) | 144 | 0.41 |
Leu | CUA(L) | 408 | 0.88 | Pro | CCU(P) | 426 | 1.6 | Gln | CAA(Q) | 729 | 1.54 | Arg | CGU(R) | 360 | 1.36 |
Leu | CUG(L) | 184 | 0.4 | Pro | CCC(P) | 200 | 0.75 | Gln | CAG(Q) | 216 | 0.46 | Arg | CGC(R) | 92 | 0.35 |
Ile | AUU(I) | 1130 | 1.5 | Pro | CCA(P) | 299 | 1.12 | Asn | AAU(N) | 960 | 1.53 | Arg | CGA(R) | 366 | 1.38 |
Ile | AUC(I) | 410 | 0.54 | Pro | CCG(P) | 143 | 0.54 | Asn | AAC(N) | 297 | 0.47 | Arg | CGG(R) | 120 | 0.45 |
Ile | AUA(I) | 718 | 0.95 | Thr | ACU(T) | 531 | 1.61 | Lys | AAA(K) | 1061 | 1.5 | Arg | AGA(R) | 475 | 1.79 |
Met | AUG(M) | 607 | 1 | Thr | ACC(T) | 250 | 0.76 | Lys | AAG(K) | 357 | 0.5 | Arg | AGG(R) | 175 | 0.66 |
Val | GUU(V) | 514 | 1.48 | Thr | ACA(T) | 402 | 1.22 | Asp | GAU(D) | 883 | 1.66 | Gly | GGU(G) | 552 | 1.26 |
Val | GUC(V) | 160 | 0.46 | Thr | ACG(T) | 134 | 0.41 | Asp | GAC(D) | 184 | 0.34 | Gly | GGC(G) | 190 | 0.43 |
Val | GUA(V) | 522 | 1.5 | Cys | UGU(C) | 235 | 1.55 | Glu | GAA(E) | 1041 | 1.53 | Gly | GGA(G) | 712 | 1.62 |
Val | GUG(V) | 194 | 0.56 | Cys | UGC(C) | 68 | 0.45 | Glu | GAG(E) | 323 | 0.47 | Gly | GGG(G) | 302 | 0.69 |
No. | Size (bp) | Type | Repeat 1 Start | Repeat 1 Location | Repeat 2 Start | Repeat 2 Location | Location |
---|---|---|---|---|---|---|---|
1 | 35 | F | 3144 | matK | 6441 | IGS (rps16, trnQ-UUG) | LSC |
2 | 30 | P | 4153 | IGS (trnK-UUU (exon), rps16) | 4211 | IGS (trnK-UUU (exon), rps16) | LSC |
3 | 30 | R | 4578 | IGS (trnK-UUU (exon), rps16) | 4581 | IGS (trnK-UUU (exon), rps16) | LSC |
4 | 30 | C | 4581 | IGS (trnK-UUU (exon), rps16) | 4582 | IGS (trnK-UUU (exon), rps16) | LSC |
5 | 30 | R | 6862 | IGS (trnQ-UUG, psbK) | 8268 | IGS (trnS-GCU, trnG-UCC) | LSC |
6 | 30 | F | 7743 | IGS (psbI, trnS-GCU) | 7770 | IGS (psbI, trnS-GCU) | LSC |
7 | 32 | F | 7896 | IGS (psbI, trnS-GCU) | 36,017 | IGS (psbC, trnS-UGA) | LSC |
8 | 30 | P | 7898 | IGS (psbI, trnS-GCU) | 46,268 | trnS-GGA | LSC |
9 | 37 | R | 8258 | IGS (trnS-GCU, trnG-UCC) | 8261 | IGS (trnS-GCU, trnG-UCC) | LSC |
10 | 37 | R | 8258 | IGS (trnS-GCU, trnG-UCC) | 8264 | IGS (trnS-GCU, trnG-UCC) | LSC |
11 | 35 | F | 8258 | IGS (trnS-GCU, trnG-UCC) | 8277 | IGS (trnS-GCU, trnG-UCC) | LSC |
12 | 35 | R | 8266 | IGS (trnS-GCU, trnG-UCC) | 8277 | IGS (trnS-GCU, trnG-UCC) | LSC |
13 | 34 | R | 8258 | IGS (trnS-GCU, trnG-UCC) | 8261 | IGS (trnS-GCU, trnG-UCC) | LSC |
14 | 33 | F | 8261 | IGS (trnS-GCU, trnG-UCC) | 8283 | IGS (trnS-GCU, trnG-UCC) | LSC |
15 | 32 | R | 8263 | IGS (trnS-GCU, trnG-UCC) | 8280 | IGS (trnS-GCU, trnG-UCC) | LSC |
16 | 31 | F | 8261 | IGS (trnS-GCU, trnG-UCC) | 8264 | IGS (trnS-GCU, trnG-UCC) | LSC |
17 | 31 | R | 8261 | IGS (trnS-GCU, trnG-UCC) | 8280 | IGS (trnS-GCU, trnG-UCC) | LSC |
18 | 31 | R | 8267 | IGS (trnS-GCU, trnG-UCC) | 29,873 | IGS (psbM, trnD-GUC) | LSC |
19 | 30 | P | 8267 | IGS (trnS-GCU, trnG-UCC) | 62,668 | IGS (ycf4, cemA) | LSC |
20 | 30 | P | 8280 | IGS (trnS-GCU, trnG-UCC) | 31,428 | IGS (trnE-UUC, trnT-GGU) | LSC |
21 | 31 | F | 9566 | trnG-UCC | 37,057 | trnG-GCC | LSC |
22 | 30 | P | 36,019 | IGS (psbC, trnS-UGA) | 46,268 | trnS-GGA | LSC |
23 | 30 | F | 39,314 | psaB | 41,538 | psaA | LSC |
24 | 42 | F | 44,540 | ycf3 (intronII) | 123,558 | ndhA (intron) | LSC, SSC |
25 | 39 | F | 44,543 | ycf3 (intronII) | 100,738 | IGS (rps12, trnV-GAC) | LSC, IRb |
26 | 39 | P | 44,543 | ycf3 (intronII) | 143,050 | IGS (trnV-GAC, rps12) | LSC, IRa |
27 | 30 | F | 44,555 | ycf3 (intronII) | 100,750 | IGS (rps12, trnV-GAC) | LSC, IRb |
28 | 30 | P | 44,555 | ycf3 (intronII) | 143,047 | IGS (trnV-GAC, rps12) | LSC, IRa |
29 | 40 | P | 76,849 | IGS (psbT, psbN) | 76,849 | IGS (psbT, psbN) | LSC |
30 | 30 | P | 84,344 | IGS (trnS-GCU, trnG-UCC) | 84,346 | IGS (trnS-GCU, trnG-UCC) | LSC |
31 | 61 | F | 93,517 | ycf2 | 93,535 | ycf2 | IRb |
32 | 61 | P | 93,517 | ycf2 | 150,231 | ycf2 | IRb, IRa |
33 | 61 | P | 93,535 | ycf2 | 150,249 | ycf2 | IRb, IRa |
34 | 61 | F | 150,231 | ycf2 | 150,249 | ycf2 | IRa |
35 | 52 | F | 93,526 | ycf2 | 93,544 | ycf2 | IRb |
36 | 52 | P | 93,526 | ycf2 | 150,231 | ycf2 | IRb, IRa |
37 | 52 | P | 93,544 | ycf2 | 150,249 | ycf2 | IRb, IRa |
38 | 34 | F | 93,526 | ycf2 | 93,562 | ycf2 | IRb |
39 | 34 | P | 93,526 | ycf2 | 150,231 | ycf2 | IRb, IRa |
40 | 34 | P | 93,562 | ycf2 | 150,267 | ycf2 | IRb, IRa |
41 | 43 | F | 93,517 | ycf2 | 93,533 | ycf2 | IRb |
42 | 43 | P | 93,517 | ycf2 | 150,231 | ycf2 | IRb, IRa |
43 | 43 | P | 93,553 | ycf2 | 150,267 | ycf2 | IRb, IRa |
44 | 43 | F | 150,231 | ycf2 | 150,267 | ycf2 | IRa |
45 | 40 | F | 100,738 | IGS (rps12, trnV-GAC) | 123,561 | ndhA (intron) | IRb, SSC |
46 | 34 | F | 109,506 | IGS (rrn4.5, rrn5) | 109,538 | IGS (rrn4.5, rrn5) | IRb |
47 | 34 | F | 109,506 | IGS (rrn4.5, rrn5) | 134,255 | IGS (rrn5, rrn4.5) | IRb, IRa |
48 | 34 | P | 109,538 | IGS (rrn4.5, rrn5) | 134,287 | IGS (rrn5, rrn4.5) | IRb, IRa |
49 | 34 | P | 134,255 | IGS (rrn5, rrn4.5) | 134,287 | IGS (rrn5, rrn4.5) | IRa |
50 | 38 | P | 118,646 | IGS (ccsA, ndhD) | 118,646 | IGS (ccsA, ndhD) | SSC |
51 | 40 | P | 123,561 | ndhA (intron) | 143,049 | IGS(trnV-GAC, rps12) | SSC, IRa |
Length Unit | 10 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | Total |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | 15 | 15 | 3 | 8 | 1 | 1 | 3 | 1 | 1 | 33 | |||
T | 14 | 14 | 4 | 7 | 3 | 2 | 1 | 1 | 1 | 33 | |||
C | 1 | 1 | 1 | ||||||||||
G | 1 | 1 | 1 | ||||||||||
AG | 1 | 1 | 1 | ||||||||||
AT | 4 | 4 | 3 | 7 | |||||||||
TA | 2 | 2 | 1 | 1 | 4 | ||||||||
AAT | 1 | 1 | 1 | ||||||||||
ATA | 1 | 1 | |||||||||||
TTA | 2 | 2 | |||||||||||
TAT | 1 | 1 | |||||||||||
AGGT | 1 | 1 | |||||||||||
ATGG | 1 | 1 | |||||||||||
AATT | 1 | 1 | |||||||||||
CTAC | 1 | 1 | |||||||||||
TTTC | 1 | 1 | |||||||||||
TAAT | 1 | 1 | |||||||||||
GGAA | 1 | 1 |
No. | Type | Motif | Size | Start | End | Location | Region |
---|---|---|---|---|---|---|---|
1 | P1 | (A)10 | 10 | 47 | 56 | trnH-UGG | LSC |
2 | P1 | (A)10 | 10 | 637 | 646 | psbA | LSC |
3 | P1 | (A)11 | 11 | 2104 | 2114 | matK | LSC |
4 | P1 | (A)12 | 12 | 3942 | 3953 | trnK-UUU (intron) | LSC |
5 | P2 | (AT)5 | 10 | 755 | 764 | psbA | LSC |
6 | P4 | (AATT)3 | 12 | 3974 | 3985 | trnK-UUU (intron) | LSC |
7 | P4 | (CCAT)3 | 12 | 54 | 65 | trnH-UGG | LSC |
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Liu, X.; Li, Y.; Yang, H.; Zhou, B. Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis. Molecules 2018, 23, 857. https://doi.org/10.3390/molecules23040857
Liu X, Li Y, Yang H, Zhou B. Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis. Molecules. 2018; 23(4):857. https://doi.org/10.3390/molecules23040857
Chicago/Turabian StyleLiu, Xia, Yuan Li, Hongyuan Yang, and Boyang Zhou. 2018. "Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis" Molecules 23, no. 4: 857. https://doi.org/10.3390/molecules23040857