Background
Methods
DNA extraction and sequencing
Genome assembly and annotation
Sequence analyses
Genome comparison
Phylogenomic analysis
Results and discussion
General characteristics of the A. compactum cp genome
T(U)% | C% | A% | G% | Length (bp) | |
---|---|---|---|---|---|
LSC | 33.8 | 17.2 | 32.5 | 16.5 | 88,535 |
IR | 28.8 | 19.8 | 30.1 | 21.3 | 29,824 |
SSC | 34.3 | 15.6 | 35.9 | 14.2 | 15,370 |
Total | 32.3 | 18.3 | 31.7 | 17.8 | 163,553 |
CDS | 31.6 | 17.2 | 31.5 | 19.8 | 79,701 |
1st position | 24 | 18.2 | 31.3 | 26.7 | 26,567 |
2nd position | 32 | 20.2 | 30.0 | 17.4 | 26,567 |
3rd position | 39 | 13.1 | 33.1 | 15.3 | 26,567 |
Gene category | Gene group | Gene name |
---|---|---|
Self-replication | rRNA genes | rrn16c, rrn23c, rrn5c, rrn4.5c |
tRNA genes | trnH-GUGc, trnK-UUUa, trnQ-UUG, trnS-GCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC, trnR-UCU, trnT-GGU, trnS-UGA, trnG-GCCc, trnfM-CAU, trnS-GGA, trnT-UGU, trnL-UAAa, trnF-GAA, trnV-UACa, trnW-CCA, trnP-UGG, trnI-CAUc, trnL-CAAc, trnV-GACc, trnI-GAUa, c, trnA-UGCa, c, trnR-ACGc, trnN-GUUc, trnL-UAG, trnM-CAU | |
Small subunit of ribosome | rps4, rps14, rps18, rps2, rps12b, c, rps11, rps8, rps3, rps19, rps7c, rps15, rps16a | |
Large subunit of ribosome | rpl33, rpl20, rpl36, rpl14, rpl16a, rpl22, rpl2a, c, rpl23c, rpl32 | |
DNA dependent RNA polymerase | rpoB, rpoC1a, rpoC2, rpoA | |
Translational initiation factor |
infA
| |
Genes for photosynthesis | Subunits of NADH dehydrogenase | ndhAa, ndhBa, c, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ, ycf3b, ycf4 | |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Subunits of cytochrome b/f complex | petN, petA, petL, petG, petBa, petD | |
Subunits of ATP synthase | atpI, atpH, atpFa, atpA, atpE, atpB | |
Large subunit of rubisco |
rbcL
| |
Genes of unknown function | Open reading frames (ORF, ycf) | ycf1, ycf15c, ycf2c |
Pseudogenes |
ycf1
|
Amino acid | Codon | No. | RSCU | tRNA | Amino acid | Codon | Count | RSCU | tRNA |
---|---|---|---|---|---|---|---|---|---|
Phe | UUU | 971 | 1.31 | Tyr | UAU | 811 | 1.57 | ||
Phe | UUC | 516 | 0.69 | trnF-GAA | Tyr | UAC | 221 | 0.43 | trnY-GUA |
Leu | UUA | 892 | 1.96 | trnL-UAA | Stop | UAA | 48 | 1.66 | |
Leu | UUG | 559 | 1.23 | trnL-CAA | Stop | UAG | 22 | 0.76 | |
Leu | CUU | 567 | 1.25 | His | CAU | 519 | 1.6 | ||
Leu | CUC | 181 | 0.4 | His | CAC | 129 | 0.4 | trnH-GUG | |
Leu | CUA | 381 | 0.84 | trnL-UAG | Gln | CAA | 706 | 1.54 | trnQ-UUG |
Leu | CUG | 151 | 0.33 | Gln | CAG | 210 | 0.46 | ||
Ile | AUU | 1146 | 1.47 | Asn | AAU | 989 | 1.55 | ||
Ile | AUC | 426 | 0.55 | trnI-GAU | Asn | AAC | 289 | 0.45 | trnN-GUU |
Ile | AUA | 763 | 0.98 | trnI-CAU | Lys | AAA | 1114 | 1.49 | trnK-UUU |
Met | AUG | 614 | 1 | trn(f)M-CAU | Lys | AAG | 383 | 0.51 | |
Val | GUU | 521 | 1.45 | Asp | GAU | 875 | 1.64 | ||
Val | GUC | 159 | 0.44 | trnV-GAC | Asp | GAC | 192 | 0.36 | trnD-GUC |
Val | GUA | 559 | 1.56 | trnV-UAC | Glu | GAA | 1125 | 1.53 | trnE-UUC |
Val | GUG | 194 | 0.54 | Glu | GAG | 350 | 0.47 | ||
Ser | UCU | 598 | 1.74 | Cys | UGU | 232 | 1.56 | ||
Ser | UCC | 337 | 0.98 | trnS-GGA | Cys | UGC | 66 | 0.44 | trnC-GCA |
Ser | UCA | 412 | 1.2 | trnS-UGA | Stop | UGA | 17 | 0.59 | |
Ser | UCG | 182 | 0.53 | Trp | UGG | 452 | 1 | trnW-CCA | |
Pro | CCU | 442 | 1.62 | Arg | CGU | 365 | 1.37 | trnR-ACG | |
Pro | CCC | 202 | 0.74 | Arg | CGC | 86 | 0.32 | ||
Pro | CCA | 325 | 1.19 | trnP-UGG | Arg | CGA | 342 | 1.29 | |
Pro | CCG | 120 | 0.44 | Arg | CGG | 113 | 0.43 | ||
Thr | ACU | 537 | 1.57 | Arg | AGA | 519 | 1.95 | trnR-UCU | |
Thr | ACC | 237 | 0.7 | trnT-GGU | Arg | AGG | 168 | 0.63 | |
Thr | ACA | 433 | 1.27 | trnT-UGU | Ser | AGU | 430 | 1.25 | |
Thr | ACG | 157 | 0.46 | Ser | AGC | 102 | 0.3 | trnS-GCU | |
Ala | GCU | 626 | 1.82 | Gly | GGU | 604 | 1.39 | ||
Ala | GCC | 203 | 0.59 | Gly | GGC | 141 | 0.33 | trnG-GCC | |
Ala | GCA | 434 | 1.26 | trnA-UGC | Gly | GGA | 714 | 1.65 | |
Ala | GCG | 112 | 0.33 | Gly | GGG | 276 | 0.64 |
Repeat and SSR analysis
cpSSR ID | Repeat motif | Length (bp) | Start | End | Region | Annotation |
---|---|---|---|---|---|---|
1 | (T)10 | 10 | 3975 | 3984 | LSC | trnK-UUU |
2 | (A)10 | 10 | 4328 | 4337 | LSC | |
3 | (TA)6 | 12 | 4900 | 4911 | LSC | |
4 | (A)10 | 10 | 5287 | 5296 | LSC | rps16 intron |
5 | (A)11 | 11 | 6253 | 6263 | LSC | |
6 | (TA)6 | 12 | 6609 | 6620 | LSC | |
7 | (A)10 | 10 | 7204 | 7213 | LSC | |
8 | (AT)6 | 12 | 7521 | 7532 | LSC | |
9 | (A)10 | 10 | 7700 | 7709 | LSC | |
10 | (T)12 | 12 | 8633 | 8644 | LSC | |
11 | (A)13 | 13 | 14,885 | 14,897 | LSC | |
12 | (T)10 | 10 | 17,474 | 17,483 | LSC | |
13 | (A)10 | 10 | 19,831 | 19,840 | LSC |
rpoC2
|
14 | (T)11 | 11 | 24,121 | 24,131 | LSC | rpoC1 intron |
15 | (A)10 | 10 | 28,802 | 28,811 | LSC | |
16 | (A)15 | 15 | 29,013 | 29,027 | LSC | |
17 | (A)11 | 11 | 30,868 | 30,878 | LSC | |
18 | (T)10 | 10 | 35,129 | 35,138 | LSC | |
19 | (TA)7 | 14 | 38,632 | 38,645 | LSC | |
20 | (A)12 | 12 | 39,292 | 39,303 | LSC | |
21 | (A)12 | 12 | 47,481 | 47,492 | LSC | |
22 | (T)10 | 10 | 48,986 | 48,995 | LSC | |
23 | (A)10 | 10 | 50,236 | 50,245 | LSC | |
24 | (AT)7 | 14 | 50,395 | 50,408 | LSC | |
25 | (T)10 | 10 | 51,829 | 51,838 | LSC | |
26 | (T)11 | 11 | 52,709 | 52,719 | LSC | |
27 | (ATA)5 | 15 | 54,345 | 54,359 | LSC | |
28 | (A)11 | 11 | 54,562 | 54,572 | LSC | |
29 | (T)10 | 10 | 58,778 | 58,787 | LSC | |
30 | (T)11 | 11 | 59,269 | 59,279 | LSC | |
31 | (A)12 | 12 | 60,919 | 60,930 | LSC | |
32 | (T)10 | 10 | 61,621 | 61,630 | LSC | |
33 | (AT)6 | 12 | 63,489 | 63,500 | LSC | |
34 | (A)12 | 12 | 68,715 | 68,726 | LSC | |
35 | (AT)10 | 20 | 69,266 | 69,285 | LSC | |
36 | (T)10 | 10 | 70,716 | 70,725 | LSC | |
37 | (A)10 | 10 | 72,600 | 72,609 | LSC |
rps18
|
38 | (TA)7 | 14 | 74,094 | 74,107 | LSC | rps12 intron |
39 | (A)10 | 10 | 74,569 | 74,578 | LSC | clpP intron |
40 | (T)11 | 11 | 74,845 | 74,855 | LSC | clpP intron |
41 | (T)10 | 10 | 75,108 | 75,117 | LSC | clpP intron |
42 | (T)10 | 10 | 75,572 | 75,581 | LSC | clpP intron |
43 | (T)10 | 10 | 75,831 | 75,840 | LSC | clpP intron |
44 | (A)10 | 10 | 79,177 | 79,186 | LSC | |
45 | (AT)6 | 12 | 79,751 | 79,762 | LSC | petB intron |
46 | (T)10 | 10 | 86,407 | 86,416 | LSC | rpl16 intron |
47 | (T)11 | 11 | 88,970 | 88,980 | IRa | |
48 | (T)10 | 10 | 116,573 | 116,582 | IRa |
ycf1
|
49 | (A)11 | 11 | 120,872 | 120,882 | SSC | |
50 | (T)11 | 11 | 121,055 | 121,065 | SSC | |
51 | (A)11 | 11 | 128,865 | 128,875 | SSC | ndhA intron |
52 | (T)10 | 10 | 129,188 | 129,197 | SSC | ndhA intron |
53 | (AT)6 | 12 | 131,778 | 131,789 | SSC | |
54 | (T)11 | 11 | 133,103 | 133,113 | SSC | |
55 | (T)12 | 12 | 133,236 | 133,247 | SSC | |
56 | (T)11 | 11 | 133,374 | 133,384 | SSC |
ycf1
|
57 | (A)10 | 10 | 135,507 | 135,516 | IRb |
ycf1
|
58 | (A)11 | 11 | 163,109 | 163,119 | IRb |
ID | Repeat start 1 | Type | Size (bp) | Repeat start 2 | Mismatch (bp) | E value | Gene | Region |
---|---|---|---|---|---|---|---|---|
1 | 3990 | P | 34 | 3996 | − 3 | 4.12E−06 | trnK-UUU (intron) | LSC |
2 | 8768 | P | 31 | 48,057 | − 3 | 1.98E−04 | IGS; trnS-GGA | LSC |
3 | 10,522 | F | 30 | 39,347 | − 3 | 7.15E−04 | trnG-GCC (intron) | LSC |
4 | 31,322 | P | 32 | 31,352 | − 3 | 5.46E−05 | IGS | LSC |
5 | 32,991 | F | 30 | 33,020 | − 3 | 7.15E−04 | IGS | LSC |
6 | 39,660 | P | 32 | 39,701 | 0 | 4.08E−10 | IGS | LSC |
7 | 41,551 | F | 58 | 43,775 | − 3 | 7.54E−20 | psaB; psaA | LSC |
8 | 41,595 | F | 37 | 43,819 | − 2 | 2.39E−09 | psaB; psaA | LSC |
9 | 63,481 | P | 31 | 126,101 | − 3 | 1.98E−04 | IGS | LSC; SSC |
10 | 63,481 | F | 31 | 126,106 | − 3 | 1.98E−04 | IGS | LSC; SSC |
11 | 63,487 | F | 32 | 69,264 | − 3 | 5.46E−05 | IGS | LSC |
12 | 67,809 | P | 31 | 67,864 | − 2 | 6.83E−06 | IGS | LSC |
13 | 71,632 | F | 30 | 71,659 | 0 | 6.53E−09 | IGS | LSC |
14 | 72,281 | F | 42 | 72,302 | − 3 | 1.21E−10 |
rps18
| LSC |
15 | 91,249 | F | 46 | 91,299 | − 1 | 2.10E−16 | trnI-CAU; IGS | IRa |
16 | 91,249 | P | 46 | 160,743 | − 1 | 2.10E−16 | trnI-CAU; IGS | IRa; IRb |
17 | 91,299 | P | 46 | 160,793 | − 1 | 2.10E−16 | IGS | IRa; IRb |
18 | 93,917 | F | 30 | 93,938 | − 3 | 7.15E−04 |
ycf2
| IRa |
19 | 93,917 | P | 30 | 158,120 | − 3 | 7.15E−04 |
ycf2
| IRa; IRb |
20 | 93,938 | P | 30 | 158,141 | − 3 | 7.15E−04 |
ycf2
| IRa; IRb |
21 | 121,695 | P | 30 | 121,723 | − 3 | 7.15E−04 | IGS | SSC |
22 | 158,122 | F | 30 | 158,143 | − 3 | 7.15E−04 |
ycf2
| IRb |
23 | 160,743 | F | 46 | 160,793 | − 1 | 2.10E−16 | IGS | IRb |
24 | 160,762 | F | 30 | 160,812 | − 3 | 7.15E−04 | IGS | IRb |