Chinese Journal of Tropical Crops ›› 2022, Vol. 43 ›› Issue (3): 439-446.DOI: 10.3969/j.issn.1000-2561.2022.03.001
• Omics & Biotechnology • Next Articles
YANG Xiangyan, CAI Yuanbao*(), TAN Qinliang, QIN Xu, HUANG Xianya, WU Mi
Received:
2021-08-09
Revised:
2021-12-06
Online:
2022-03-25
Published:
2022-03-23
Contact:
CAI Yuanbao
CLC Number:
YANG Xiangyan, CAI Yuanbao, TAN Qinliang, QIN Xu, HUANG Xianya, WU Mi. Analysis of Codon Usage Bias in the Chloroplast Genome of Ananas comosus[J]. Chinese Journal of Tropical Crops, 2022, 43(3): 439-446.
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URL: http://www.rdzwxb.com/EN/10.3969/j.issn.1000-2561.2022.03.001
基因Gene | GC1/% | GC2/% | GC3/% | GCall/% | ENC | 基因Gene | GC1/% | GC2/% | GC3/% | GCall/% | ENC |
---|---|---|---|---|---|---|---|---|---|---|---|
psbA | 48.87 | 44.07 | 32.77 | 41.90 | 42.70 | rpl20 | 37.29 | 41.53 | 27.97 | 35.59 | 49.88 |
matK | 41.21 | 31.45 | 26.95 | 33.20 | 48.93 | clpP | 59.31 | 36.27 | 32.35 | 42.65 | 61.00 |
atpA | 55.91 | 40.16 | 27.17 | 41.08 | 46.35 | psbB | 53.83 | 46.17 | 28.29 | 42.76 | 46.85 |
atpF | 49.73 | 34.05 | 30.27 | 38.02 | 42.60 | petB | 48.61 | 41.20 | 31.02 | 40.28 | 43.24 |
atpI | 48.79 | 36.29 | 29.03 | 38.04 | 48.16 | petD | 48.94 | 39.36 | 29.26 | 39.18 | 40.57 |
rps2 | 41.77 | 44.30 | 32.91 | 39.66 | 50.03 | rpoA | 46.18 | 33.53 | 27.65 | 35.78 | 48.19 |
rpoC2 | 45.82 | 37.09 | 28.14 | 37.01 | 49.74 | rps11 | 53.96 | 55.40 | 20.14 | 43.17 | 38.64 |
rpoC1 | 50.36 | 37.99 | 28.38 | 38.91 | 50.08 | rps8 | 40.74 | 40.74 | 22.96 | 34.81 | 44.02 |
rpoB | 50.05 | 38.12 | 28.52 | 38.89 | 48.10 | rpl14 | 55.28 | 36.59 | 21.95 | 37.94 | 42.39 |
psbD | 52.82 | 43.50 | 33.33 | 43.22 | 45.51 | rpl16 | 53.28 | 54.01 | 24.82 | 44.04 | 39.42 |
psbC | 54.01 | 46.20 | 33.97 | 44.73 | 46.02 | rps3 | 45.21 | 33.33 | 24.20 | 34.25 | 47.52 |
rps14 | 42.57 | 46.53 | 29.70 | 39.60 | 38.48 | rpl22 | 41.86 | 37.98 | 24.81 | 34.88 | 51.05 |
psaB | 48.03 | 42.86 | 32.38 | 41.09 | 48.64 | rpl2 | 50.73 | 50.73 | 31.75 | 44.40 | 50.07 |
psaA | 52.46 | 43.28 | 34.62 | 43.45 | 51.97 | ycf2 | 41.71 | 34.53 | 37.29 | 37.84 | 52.87 |
ycf3 | 47.37 | 39.18 | 29.82 | 38.79 | 56.52 | ndhB | 41.88 | 39.33 | 31.51 | 37.57 | 45.63 |
rps4 | 49.01 | 38.61 | 25.74 | 37.79 | 49.46 | rps7 | 52.56 | 45.51 | 21.79 | 39.96 | 44.01 |
ndhJ | 48.12 | 37.50 | 30.00 | 38.54 | 48.64 | ndhF | 37.72 | 37.58 | 21.17 | 32.16 | 42.88 |
ndhK | 40.96 | 44.03 | 31.74 | 38.91 | 53.96 | ccsA | 32.19 | 38.75 | 26.88 | 32.60 | 49.33 |
ndhC | 50.41 | 34.71 | 31.40 | 38.84 | 53.28 | ndhD | 39.44 | 37.45 | 30.48 | 35.79 | 47.28 |
atpE | 52.59 | 41.48 | 31.11 | 41.73 | 45.90 | ndhE | 38.24 | 32.35 | 27.45 | 32.68 | 45.65 |
atpB | 56.11 | 41.48 | 28.86 | 42.15 | 47.20 | ndhG | 41.24 | 35.03 | 28.81 | 35.03 | 48.47 |
rbcL | 57.50 | 43.12 | 28.75 | 43.12 | 47.72 | ndhI | 40.88 | 35.91 | 21.55 | 32.78 | 45.63 |
accD | 39.47 | 38.24 | 26.38 | 34.70 | 44.95 | ndhA | 42.98 | 38.84 | 23.97 | 35.26 | 45.45 |
ycf4 | 45.41 | 42.16 | 31.89 | 39.82 | 49.56 | ndhH | 50.76 | 35.53 | 27.66 | 37.99 | 46.99 |
cemA | 41.30 | 27.83 | 32.17 | 33.77 | 47.58 | ycf1 | 36.53 | 29.35 | 28.12 | 31.33 | 49.16 |
petA | 54.52 | 35.51 | 28.35 | 39.46 | 48.28 | 平均值 | 46.78 | 39.61 | 28.53 | 38.31 | 47.21 |
rps18 | 36.27 | 43.14 | 25.49 | 34.97 | 38.53 |
Tab. 1 GC contents and ENCs of 52 gene codons from A. comosus chloroplast genome
基因Gene | GC1/% | GC2/% | GC3/% | GCall/% | ENC | 基因Gene | GC1/% | GC2/% | GC3/% | GCall/% | ENC |
---|---|---|---|---|---|---|---|---|---|---|---|
psbA | 48.87 | 44.07 | 32.77 | 41.90 | 42.70 | rpl20 | 37.29 | 41.53 | 27.97 | 35.59 | 49.88 |
matK | 41.21 | 31.45 | 26.95 | 33.20 | 48.93 | clpP | 59.31 | 36.27 | 32.35 | 42.65 | 61.00 |
atpA | 55.91 | 40.16 | 27.17 | 41.08 | 46.35 | psbB | 53.83 | 46.17 | 28.29 | 42.76 | 46.85 |
atpF | 49.73 | 34.05 | 30.27 | 38.02 | 42.60 | petB | 48.61 | 41.20 | 31.02 | 40.28 | 43.24 |
atpI | 48.79 | 36.29 | 29.03 | 38.04 | 48.16 | petD | 48.94 | 39.36 | 29.26 | 39.18 | 40.57 |
rps2 | 41.77 | 44.30 | 32.91 | 39.66 | 50.03 | rpoA | 46.18 | 33.53 | 27.65 | 35.78 | 48.19 |
rpoC2 | 45.82 | 37.09 | 28.14 | 37.01 | 49.74 | rps11 | 53.96 | 55.40 | 20.14 | 43.17 | 38.64 |
rpoC1 | 50.36 | 37.99 | 28.38 | 38.91 | 50.08 | rps8 | 40.74 | 40.74 | 22.96 | 34.81 | 44.02 |
rpoB | 50.05 | 38.12 | 28.52 | 38.89 | 48.10 | rpl14 | 55.28 | 36.59 | 21.95 | 37.94 | 42.39 |
psbD | 52.82 | 43.50 | 33.33 | 43.22 | 45.51 | rpl16 | 53.28 | 54.01 | 24.82 | 44.04 | 39.42 |
psbC | 54.01 | 46.20 | 33.97 | 44.73 | 46.02 | rps3 | 45.21 | 33.33 | 24.20 | 34.25 | 47.52 |
rps14 | 42.57 | 46.53 | 29.70 | 39.60 | 38.48 | rpl22 | 41.86 | 37.98 | 24.81 | 34.88 | 51.05 |
psaB | 48.03 | 42.86 | 32.38 | 41.09 | 48.64 | rpl2 | 50.73 | 50.73 | 31.75 | 44.40 | 50.07 |
psaA | 52.46 | 43.28 | 34.62 | 43.45 | 51.97 | ycf2 | 41.71 | 34.53 | 37.29 | 37.84 | 52.87 |
ycf3 | 47.37 | 39.18 | 29.82 | 38.79 | 56.52 | ndhB | 41.88 | 39.33 | 31.51 | 37.57 | 45.63 |
rps4 | 49.01 | 38.61 | 25.74 | 37.79 | 49.46 | rps7 | 52.56 | 45.51 | 21.79 | 39.96 | 44.01 |
ndhJ | 48.12 | 37.50 | 30.00 | 38.54 | 48.64 | ndhF | 37.72 | 37.58 | 21.17 | 32.16 | 42.88 |
ndhK | 40.96 | 44.03 | 31.74 | 38.91 | 53.96 | ccsA | 32.19 | 38.75 | 26.88 | 32.60 | 49.33 |
ndhC | 50.41 | 34.71 | 31.40 | 38.84 | 53.28 | ndhD | 39.44 | 37.45 | 30.48 | 35.79 | 47.28 |
atpE | 52.59 | 41.48 | 31.11 | 41.73 | 45.90 | ndhE | 38.24 | 32.35 | 27.45 | 32.68 | 45.65 |
atpB | 56.11 | 41.48 | 28.86 | 42.15 | 47.20 | ndhG | 41.24 | 35.03 | 28.81 | 35.03 | 48.47 |
rbcL | 57.50 | 43.12 | 28.75 | 43.12 | 47.72 | ndhI | 40.88 | 35.91 | 21.55 | 32.78 | 45.63 |
accD | 39.47 | 38.24 | 26.38 | 34.70 | 44.95 | ndhA | 42.98 | 38.84 | 23.97 | 35.26 | 45.45 |
ycf4 | 45.41 | 42.16 | 31.89 | 39.82 | 49.56 | ndhH | 50.76 | 35.53 | 27.66 | 37.99 | 46.99 |
cemA | 41.30 | 27.83 | 32.17 | 33.77 | 47.58 | ycf1 | 36.53 | 29.35 | 28.12 | 31.33 | 49.16 |
petA | 54.52 | 35.51 | 28.35 | 39.46 | 48.28 | 平均值 | 46.78 | 39.61 | 28.53 | 38.31 | 47.21 |
rps18 | 36.27 | 43.14 | 25.49 | 34.97 | 38.53 |
参数Parameter | GC1 | GC2 | GC3 | GCall | ENC |
---|---|---|---|---|---|
GC2 | 0.347* | ||||
GC3 | 0.128 | -0.034 | |||
GCall | 0.823** | 0.709** | 0.407** | ||
ENC | 0.041 | -0.341* | 0.446** | 0.005 | |
N | -0.133 | -0.254 | 0.285* | -0.112 | 0.242 |
Tab. 2 Correlation analysis of main parameters of gene codons from A. comosus chloroplast genome
参数Parameter | GC1 | GC2 | GC3 | GCall | ENC |
---|---|---|---|---|---|
GC2 | 0.347* | ||||
GC3 | 0.128 | -0.034 | |||
GCall | 0.823** | 0.709** | 0.407** | ||
ENC | 0.041 | -0.341* | 0.446** | 0.005 | |
N | -0.133 | -0.254 | 0.285* | -0.112 | 0.242 |
氨基酸 Amino acid | 密码子 Codon | 基因组 Genome | 高表达基因 High expression gene | 低表达基因 Low expression gene | ΔRSCU | |||
---|---|---|---|---|---|---|---|---|
数目Number | RSCU | 数目Number | RSCU | 数目Number | RSCU | |||
Phe | UUU** | 733 | 1.25 | 18 | 1.38 | 102 | 1.04 | 0.34 |
UUC | 444 | 0.75 | 8 | 0.62 | 95 | 0.96 | -0.34 | |
Leu | UUA*** | 692 | 1.90 | 20 | 2.22 | 59 | 1.14 | 1.08 |
UUG** | 466 | 1.28 | 17 | 1.89 | 77 | 1.49 | 0.40 | |
CUU | 463 | 1.27 | 12 | 1.33 | 77 | 1.49 | -0.16 | |
CUC | 141 | 0.39 | 2 | 0.22 | 27 | 0.52 | -0.30 | |
CUA | 299 | 0.82 | 3 | 0.33 | 44 | 0.85 | -0.52 | |
CUG | 121 | 0.33 | 0 | 0 | 26 | 0.50 | -0.50 | |
Ile | AUU* | 891 | 1.44 | 25 | 1.42 | 108 | 1.34 | 0.08 |
AUC | 393 | 0.63 | 7 | 0.40 | 59 | 0.73 | -0.33 | |
AUA* | 574 | 0.93 | 21 | 1.19 | 74 | 0.92 | 0.27 | |
Val | GUU | 430 | 1.47 | 15 | 1.58 | 52 | 1.54 | 0.04 |
GUC | 124 | 0.42 | 1 | 0.11 | 22 | 0.65 | -0.54 | |
GUA*** | 452 | 1.55 | 20 | 2.11 | 37 | 1.10 | 1.01 | |
GUG | 162 | 0.55 | 2 | 0.21 | 24 | 0.71 | -0.50 | |
Ser | UCU | 445 | 1.65 | 7 | 0.95 | 78 | 1.54 | -0.59 |
UCC* | 269 | 1.00 | 9 | 1.23 | 57 | 1.13 | 0.10 | |
UCA | 341 | 1.27 | 11 | 1.50 | 74 | 1.46 | 0.04 | |
UCG | 150 | 0.56 | 4 | 0.55 | 32 | 0.63 | -0.08 | |
AGU*** | 334 | 1.24 | 12 | 1.64 | 48 | 0.95 | 0.69 | |
AGC | 78 | 0.29 | 1 | 0.14 | 15 | 0.30 | -0.16 | |
Pro | CCU** | 340 | 1.56 | 19 | 1.69 | 40 | 1.23 | 0.46 |
CCC* | 181 | 0.83 | 10 | 0.89 | 25 | 0.77 | 0.12 | |
CCA | 253 | 1.16 | 12 | 1.07 | 42 | 1.29 | -0.22 | |
CCG | 99 | 0.45 | 4 | 0.36 | 23 | 0.71 | -0.35 | |
Thr | ACU | 429 | 1.56 | 11 | 1.29 | 47 | 1.36 | -0.07 |
ACC* | 206 | 0.75 | 6 | 0.71 | 21 | 0.61 | 0.10 | |
ACA*** | 342 | 1.25 | 16 | 1.88 | 46 | 1.33 | 0.55 | |
ACG | 120 | 0.44 | 1 | 0.12 | 24 | 0.70 | -0.58 | |
氨基酸 Amino acid | 密码子 Codon | 基因组 Genome | 高表达基因 High expression gene | 低表达基因 Low expression gene | ΔRSCU | |||
数目Number | RSCU | 数目Number | RSCU | 数目Number | RSCU | |||
Ala | GCU | 534 | 1.84 | 18 | 1.50 | 44 | 1.69 | -0.19 |
GCC | 168 | 0.58 | 3 | 0.25 | 16 | 0.62 | -0.37 | |
GCA** | 332 | 1.15 | 17 | 1.42 | 27 | 1.04 | 0.38 | |
GCG* | 125 | 0.43 | 10 | 0.83 | 17 | 0.65 | 0.18 | |
Tyr | UAU | 660 | 1.59 | 11 | 1.47 | 94 | 1.61 | -0.14 |
UAC* | 170 | 0.41 | 4 | 0.53 | 23 | 0.39 | 0.14 | |
His | CAU** | 409 | 1.54 | 12 | 1.85 | 53 | 1.45 | 0.40 |
CAC | 121 | 0.46 | 1 | 0.15 | 20 | 0.55 | -0.40 | |
Gln | CAA* | 582 | 1.51 | 16 | 1.60 | 78 | 1.33 | 0.27 |
CAG | 189 | 0.49 | 4 | 0.40 | 39 | 0.67 | -0.27 | |
Asn | AAU | 793 | 1.57 | 21 | 1.62 | 127 | 1.56 | 0.06 |
AAC | 216 | 0.43 | 5 | 0.38 | 36 | 0.44 | -0.06 | |
Lys | AAA** | 796 | 1.49 | 32 | 1.52 | 106 | 1.18 | 0.34 |
AAG | 270 | 0.51 | 10 | 0.48 | 74 | 0.82 | -0.34 | |
Asp | GAU | 714 | 1.61 | 13 | 1.63 | 145 | 1.67 | -0.04 |
GAC | 174 | 0.39 | 3 | 0.38 | 29 | 0.33 | 0.05 | |
Glu | GAA* | 848 | 1.47 | 18 | 1.50 | 120 | 1.28 | 0.22 |
GAG | 309 | 0.53 | 6 | 0.50 | 68 | 0.72 | -0.22 | |
Cys | UGU*** | 184 | 1.48 | 5 | 2.00 | 30 | 1.40 | 0.60 |
UGC | 65 | 0.52 | 0 | 0 | 13 | 0.60 | -0.60 | |
Trp | UGG | 386 | 1.00 | 10 | 1.00 | 54 | 1.00 | 0 |
Arg | CGU*** | 294 | 1.38 | 19 | 1.52 | 22 | 0.70 | 0.82 |
CGC | 76 | 0.36 | 3 | 0.24 | 13 | 0.41 | -0.17 | |
CGA | 287 | 1.35 | 19 | 1.52 | 46 | 1.46 | 0.06 | |
CGG | 87 | 0.41 | 3 | 0.24 | 21 | 0.67 | -0.43 | |
AGA** | 409 | 1.92 | 28 | 2.24 | 60 | 1.90 | 0.34 | |
AGG | 122 | 0.57 | 3 | 0.24 | 27 | 0.86 | -0.62 | |
Gly | GGU*** | 506 | 1.37 | 21 | 1.53 | 30 | 0.86 | 0.67 |
GGC | 135 | 0.37 | 7 | 0.51 | 16 | 0.46 | 0.05 | |
GGA | 603 | 1.64 | 21 | 1.53 | 60 | 1.73 | -0.20 | |
GGG | 230 | 0.62 | 6 | 0.44 | 33 | 0.95 | -0.51 |
Tab. 3 RSCU analysis and optimal codon analysis of each amino acid in A. comosus chloroplast genome
氨基酸 Amino acid | 密码子 Codon | 基因组 Genome | 高表达基因 High expression gene | 低表达基因 Low expression gene | ΔRSCU | |||
---|---|---|---|---|---|---|---|---|
数目Number | RSCU | 数目Number | RSCU | 数目Number | RSCU | |||
Phe | UUU** | 733 | 1.25 | 18 | 1.38 | 102 | 1.04 | 0.34 |
UUC | 444 | 0.75 | 8 | 0.62 | 95 | 0.96 | -0.34 | |
Leu | UUA*** | 692 | 1.90 | 20 | 2.22 | 59 | 1.14 | 1.08 |
UUG** | 466 | 1.28 | 17 | 1.89 | 77 | 1.49 | 0.40 | |
CUU | 463 | 1.27 | 12 | 1.33 | 77 | 1.49 | -0.16 | |
CUC | 141 | 0.39 | 2 | 0.22 | 27 | 0.52 | -0.30 | |
CUA | 299 | 0.82 | 3 | 0.33 | 44 | 0.85 | -0.52 | |
CUG | 121 | 0.33 | 0 | 0 | 26 | 0.50 | -0.50 | |
Ile | AUU* | 891 | 1.44 | 25 | 1.42 | 108 | 1.34 | 0.08 |
AUC | 393 | 0.63 | 7 | 0.40 | 59 | 0.73 | -0.33 | |
AUA* | 574 | 0.93 | 21 | 1.19 | 74 | 0.92 | 0.27 | |
Val | GUU | 430 | 1.47 | 15 | 1.58 | 52 | 1.54 | 0.04 |
GUC | 124 | 0.42 | 1 | 0.11 | 22 | 0.65 | -0.54 | |
GUA*** | 452 | 1.55 | 20 | 2.11 | 37 | 1.10 | 1.01 | |
GUG | 162 | 0.55 | 2 | 0.21 | 24 | 0.71 | -0.50 | |
Ser | UCU | 445 | 1.65 | 7 | 0.95 | 78 | 1.54 | -0.59 |
UCC* | 269 | 1.00 | 9 | 1.23 | 57 | 1.13 | 0.10 | |
UCA | 341 | 1.27 | 11 | 1.50 | 74 | 1.46 | 0.04 | |
UCG | 150 | 0.56 | 4 | 0.55 | 32 | 0.63 | -0.08 | |
AGU*** | 334 | 1.24 | 12 | 1.64 | 48 | 0.95 | 0.69 | |
AGC | 78 | 0.29 | 1 | 0.14 | 15 | 0.30 | -0.16 | |
Pro | CCU** | 340 | 1.56 | 19 | 1.69 | 40 | 1.23 | 0.46 |
CCC* | 181 | 0.83 | 10 | 0.89 | 25 | 0.77 | 0.12 | |
CCA | 253 | 1.16 | 12 | 1.07 | 42 | 1.29 | -0.22 | |
CCG | 99 | 0.45 | 4 | 0.36 | 23 | 0.71 | -0.35 | |
Thr | ACU | 429 | 1.56 | 11 | 1.29 | 47 | 1.36 | -0.07 |
ACC* | 206 | 0.75 | 6 | 0.71 | 21 | 0.61 | 0.10 | |
ACA*** | 342 | 1.25 | 16 | 1.88 | 46 | 1.33 | 0.55 | |
ACG | 120 | 0.44 | 1 | 0.12 | 24 | 0.70 | -0.58 | |
氨基酸 Amino acid | 密码子 Codon | 基因组 Genome | 高表达基因 High expression gene | 低表达基因 Low expression gene | ΔRSCU | |||
数目Number | RSCU | 数目Number | RSCU | 数目Number | RSCU | |||
Ala | GCU | 534 | 1.84 | 18 | 1.50 | 44 | 1.69 | -0.19 |
GCC | 168 | 0.58 | 3 | 0.25 | 16 | 0.62 | -0.37 | |
GCA** | 332 | 1.15 | 17 | 1.42 | 27 | 1.04 | 0.38 | |
GCG* | 125 | 0.43 | 10 | 0.83 | 17 | 0.65 | 0.18 | |
Tyr | UAU | 660 | 1.59 | 11 | 1.47 | 94 | 1.61 | -0.14 |
UAC* | 170 | 0.41 | 4 | 0.53 | 23 | 0.39 | 0.14 | |
His | CAU** | 409 | 1.54 | 12 | 1.85 | 53 | 1.45 | 0.40 |
CAC | 121 | 0.46 | 1 | 0.15 | 20 | 0.55 | -0.40 | |
Gln | CAA* | 582 | 1.51 | 16 | 1.60 | 78 | 1.33 | 0.27 |
CAG | 189 | 0.49 | 4 | 0.40 | 39 | 0.67 | -0.27 | |
Asn | AAU | 793 | 1.57 | 21 | 1.62 | 127 | 1.56 | 0.06 |
AAC | 216 | 0.43 | 5 | 0.38 | 36 | 0.44 | -0.06 | |
Lys | AAA** | 796 | 1.49 | 32 | 1.52 | 106 | 1.18 | 0.34 |
AAG | 270 | 0.51 | 10 | 0.48 | 74 | 0.82 | -0.34 | |
Asp | GAU | 714 | 1.61 | 13 | 1.63 | 145 | 1.67 | -0.04 |
GAC | 174 | 0.39 | 3 | 0.38 | 29 | 0.33 | 0.05 | |
Glu | GAA* | 848 | 1.47 | 18 | 1.50 | 120 | 1.28 | 0.22 |
GAG | 309 | 0.53 | 6 | 0.50 | 68 | 0.72 | -0.22 | |
Cys | UGU*** | 184 | 1.48 | 5 | 2.00 | 30 | 1.40 | 0.60 |
UGC | 65 | 0.52 | 0 | 0 | 13 | 0.60 | -0.60 | |
Trp | UGG | 386 | 1.00 | 10 | 1.00 | 54 | 1.00 | 0 |
Arg | CGU*** | 294 | 1.38 | 19 | 1.52 | 22 | 0.70 | 0.82 |
CGC | 76 | 0.36 | 3 | 0.24 | 13 | 0.41 | -0.17 | |
CGA | 287 | 1.35 | 19 | 1.52 | 46 | 1.46 | 0.06 | |
CGG | 87 | 0.41 | 3 | 0.24 | 21 | 0.67 | -0.43 | |
AGA** | 409 | 1.92 | 28 | 2.24 | 60 | 1.90 | 0.34 | |
AGG | 122 | 0.57 | 3 | 0.24 | 27 | 0.86 | -0.62 | |
Gly | GGU*** | 506 | 1.37 | 21 | 1.53 | 30 | 0.86 | 0.67 |
GGC | 135 | 0.37 | 7 | 0.51 | 16 | 0.46 | 0.05 | |
GGA | 603 | 1.64 | 21 | 1.53 | 60 | 1.73 | -0.20 | |
GGG | 230 | 0.62 | 6 | 0.44 | 33 | 0.95 | -0.51 |
组限 Class boundary | 组中值 Class mid value | 频数 Frequency number | 频率 Frequency/% |
---|---|---|---|
-0.25 ~ -0.15 | -0.20 | 1 | 1.9 |
-0.15 ~ -0.05 | -0.10 | 4 | 7.7 |
-0.05 ~ 0.05 | 0 | 32 | 61.5 |
0.05 ~ 0.15 | 0.10 | 10 | 19.2 |
0.15 ~ 0.25 | 0.20 | 5 | 9.6 |
合计 | 52 | 100.0 |
Tab. 4 Distribution of ENC ration
组限 Class boundary | 组中值 Class mid value | 频数 Frequency number | 频率 Frequency/% |
---|---|---|---|
-0.25 ~ -0.15 | -0.20 | 1 | 1.9 |
-0.15 ~ -0.05 | -0.10 | 4 | 7.7 |
-0.05 ~ 0.05 | 0 | 32 | 61.5 |
0.05 ~ 0.15 | 0.10 | 10 | 19.2 |
0.15 ~ 0.25 | 0.20 | 5 | 9.6 |
合计 | 52 | 100.0 |
[1] |
ALVES-PEREIRA A, CLEMENT C R, PICANÇO- RODRIGUES D, VEASEY E A, DEQUIGIOVANNI G, RAMOS S L F, PINHEIRO J B, ZUCCHI M I. Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers[J]. Annals of Botany, 2018, 121(4):625-639.
DOI URL |
[2] |
MEUCCI S, SCHULTE L, ZIMMERMANN H H, STOOF- LEICHSENRING K R, EPP L, BRONKEN EIDESEN P, HERZSCHUH U. Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses[J]. Ecology and Evolution, 2021, 11(5):2173-2193.
DOI URL |
[3] |
WANG K, CUI Y, WANG Y, GAO Z, LIU T, MENG C, QIN S. Chloroplast genetic engineering of a unicellular green alga Haematococcus pluvialis with expression of an antimicrobial peptide[J]. Marine Biotechnology, 2020, 22(4):572-580.
DOI URL |
[4] |
WANNATHONG T, WATERHOUSE J C, YOUNG R E, ECONOMOU C K, PURTON S. New tools for chloroplast genetic engineering allow the synjournal of human growth hormone in the green alga Chlamydomonas reinhardtii[J]. Applied Microbiology and Biotechnology, 2016, 100(12):5467-5477.
DOI URL |
[5] |
LIU H, LU Y, LAN B, XU J. Codon usage by chloroplast gene is bias in Hemiptelea davidii[J]. Journal of Genetics, 2020, 99:8.
DOI URL |
[6] |
KONG W Q, YANG J H. The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within Genus morus L[J]. PeerJ, 2017, 5(31):e3037.
DOI URL |
[7] |
WANG Z, XU B, LI B, ZHOU Q, WANG G, JIANG X, WANG C, XU Z. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species[J]. PeerJ, 2020, 8:e8251.
DOI URL |
[8] |
QUAX T E, CLAASSENS N J, SÖLL D, OOST J. Codon bias as a means to fine-tune gene expression[J]. Molecular Cell, 2015, 59(2):149-161.
DOI URL |
[9] | BHATTACHARYYA D, UDDIN A, DAS S, CHAKRABORTY S. Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae)[J]. Mitochondrial DNA, 2019, 30(4):664-673. |
[10] |
WU S, XU L, HUANG R, WANG Q. Improved biohydrogen production with an expression of codon-optimized hemH and lba genes in the chloroplast of Chlamydomonas reinhardtii[J]. Bioresource Technology, 2011, 102(3):2610-2616.
DOI URL |
[11] |
KWON K C, CHAN H T, LEÓN I R, WILLIAMS- CARRIER R, BARKAN A, DANIELL H. Codon optimization to enhance expression yields insights into chloroplast translation[J]. Plant Physiology, 2016, 172(1):62-77.
DOI URL |
[12] |
CHAKRABORTY S, YENGKHOM S, UDDIN A. Analysis of codon usage bias of chloroplast genes in Oryza species: codon usage of chloroplast genes in Oryza species[J]. Planta, 2020, 252(4):1-20.
DOI URL |
[13] | TIAN G, LI G, LIU Y, LIU Q, WANG Y, XIA G, WANG M. Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat[J]. PLoS One, 2020, 15(11):e0242624. |
[14] | REDWAN R M, SAIDIN A, KUMAR S V. Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae[J]. BMC Plant Biology, 2015, 15(196):1-20. |
[15] |
REDWAN R M, SAIDIN A, KUMAR S V. Erratum to: Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae[J]. BMC Plant Biology, 2015, 15:294.
DOI URL |
[16] | 陈哲, 胡福初, 王祥和, 范鸿雁, 张治礼. 菠萝密码子使用偏好性分析[J]. 果树学报, 2017, 34(8):946-955. |
CHEN Z, HU F C, WANG X H, FAN H Y, ZHANG Z L. Analysis of codon usage bias of Ananas comosus with genome sequencing data[J]. Journal of Fruit Science, 2017, 34(8):946-955. (in Chinese) | |
[17] | 杨祥燕, 蔡元保, 张治礼, 孙光明, 孙伟生, 吴青松, 王运儒. 菠萝MADS-box基因AcMADS2的克隆与表达分析[J]. 植物生理学报, 2016, 52(9):1406-1412. |
YANG X Y, CAI Y B, ZHANG Z L, SUN G M, SUN W S, WU Q S, WANG Y R. Cloning and expression analysis of MADS-box gene AcMADS2 from pineapple (Ananas comosus)[J]. Plant Physiology Journal, 2016, 52(9):1406-1412. (in Chinese) | |
[18] |
蔡元保, 杨祥燕, 孙光明, 黄强, 刘业强, 李绍鹏, 张治礼. 菠萝花发育相关基因AcMADS1的克隆与组织表达特性分析[J]. 植物学报, 2014, 49(6):692-703.
DOI |
CAI Y B, YANG X Y, SUN G M, HUANG Q, LIU Y Q, LI S P, ZHANG Z L. Cloning of flowering-related gene AcMADS1 and characterization of expression in tissues of pineapple (Ananas comosus)[J]. Chinese Bulletin of Botany, 2014, 49(6):692-703. (in Chinese) | |
[19] |
PAUL P, MALAKAR A K, CHAKRABORTY S. Codon usage and amino acid usage influence genes expression level[J]. Genetica, 2018, 146(1):53-63.
DOI URL |
[20] | 李显煌, 杨生超, 辛雅萱, 屈亚亚, 杨琳懿, 冯发玉, 范伟, 辛培尧. 灯盏花叶绿体基因组密码子偏好性分析[J]. 云南农业大学学报(自然科学), 2021, 36(3):384-392. |
LI X H, YANG S C, XIN Y X, QU Y Y, YANG L Y, FENG F Y, FAN W, XIN P Y. Analysis of the codon usage bias of chloroplast genome in Erigeron breviscapus (Vant.) Hand- Mazz[J]. Journal of Yunnan Agricultural University (Natural Science), 2021, 36(3):384-392. (in Chinese) | |
[21] |
LI G, PAN Z, GAO S, HE Y, XIA Q, JIN Y, YAO H. Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis[J]. Genes and Genomics, 2019, 41(10):1173-1181.
DOI URL |
[22] | 尚明照, 刘方, 华金平, 王坤波. 陆地棉叶绿体基因组密码子使用偏性的分析[J]. 中国农业科学, 2011, 44(2):245-253. |
SHANG M Z, LIU F, HUA J P, WANG K B. Analysis on codon usage of chloroplast genome of Gossypium hirsutum[J]. Scientia Agricultura Sinica, 2011, 44(2):245-253. (in Chinese) | |
[23] | 王鹏良, 吴双成, 杨利平, 王华宇, 陈乃明, 张照远. 巨桉叶绿体基因组密码子偏好性分析[J]. 广西植物, 2019, 39(12):1583-1592. |
WANG P L, WU S C, YANG L P, WANG H Y, CHEN N M, ZHANG Z Y. Analysis of codon bias of chloroplast genome in Eucalyptus grandis[J]. Guihaia, 2019, 39(12):1583-1592. (in Chinese) | |
[24] | 唐玉娟, 赵英, 黄国弟, 付海天, 宋恩亮, 李日旺, 金刚. 芒果叶绿体基因组密码子使用偏好性分析[J]. 热带作物学报, 2021, 42(8):2143-2150. |
TANG Y J, ZHAO Y, HUANG G D, FU H T, SONG E L, LI R W, JIN G. Analysis on codon usage bias of chloroplast genes from mango[J]. Chinese Journal of Tropical Crops, 2021, 42(8):2143-2150. (in Chinese) | |
[25] |
WANG L, ROOSSINCK M J. Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants[J]. Plant Molecular Biology, 2006, 61:699-710.
DOI URL |
[26] | 刘慧, 王梦醒, 岳文杰, 邢光伟, 葛玲巧, 聂小军, 宋卫宁. 糜子叶绿体基因组密码子使用偏性的分析[J]. 植物科学学报, 2017, 35(3):362-371. |
LIU H, WANG M X, YUE W J, XING G W, GE L Q, NIE X J, SONG W N. Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)[J]. Plant Science Journal, 2017, 35(3):362-371. (in Chinese) | |
[27] | 李冬梅, 吕复兵, 朱根发, 操君喜, 孙映波, 刘海林, 王真. 文心兰叶绿体基因组密码子使用的相关分析[J]. 广东农业科学, 2012, 39(10):61-65. |
LI D M, LV F B, ZHU G F, CAO J X, SUN Y B, LIU H L, WANG Z. Analysis on codon usage of chloroplast genome of Oncidium Gower Ramsey[J]. Guangdong Agricultural Science, 2012, 39(10):61-65. (in Chinese) | |
[28] | 王媛媛, 杨美青. 蒙古韭叶绿体基因组密码子使用偏好性分析[J]. 分子植物育种, 2021, 19(4):1084-1092. |
WANG Y Y, YANG M Q. Analysis of the codon usage bias in the chloroplast genome of Allium mongolicum Regel[J]. Molecular Plant Breeding, 2021, 19(4):1084-1092. (in Chinese) |
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