Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (6): 233-247.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1369
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YIN Ming-hua1,2,3,4(), YU Huan-yuan1, XIAO Xin-yi1, WANG Yu-ting1
Received:
2022-11-07
Online:
2023-06-26
Published:
2023-07-07
Contact:
YIN Ming-hua
E-mail:yinminghua04@163.com
YIN Ming-hua, YU Huan-yuan, XIAO Xin-yi, WANG Yu-ting. Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan[J]. Biotechnology Bulletin, 2023, 39(6): 233-247.
基因分类 Category | 基因分组 Gene group | 基因名称 Gene name |
---|---|---|
光合作用 Photosynthesis | 光合系统I基因 Photosystem I | psaA、psaB、psaC、psaI、psaJ |
光合系统II基因 Photosystem II | psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ | |
细胞色素复合物基因 Cytochrome b/f complex | petA、petB、petD、petG、petL、petN | |
ATP合成酶基因 ATP synthase | atpA、atpB、atpE、atpF、atpH、atpI | |
NADH脱氢酶基因 NADH dehydrogenase | ndhA、ndhB(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK | |
二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit | rbcL | |
自我复制Self-replication | RNA聚合酶亚基基因RNA polymeras | rpoA、rpoB、rpoC1、rpoC2 |
核糖体小亚基基因 Ribosomal proteins(SSU) | rps11、rps12(2)、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7(2)、rps8 | |
核糖体大亚基基因 Ribosomal proteins(LSU) | rpl14、rpl16、rpl2(2)、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36、 | |
转运RNA基因 Transfer RNAs | trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU(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-UGU、trnV-GAC(2)、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU | |
核糖体RNA基因 Ribosomal RNAs | rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2) | |
其他基因 Other genes | 成熟酶基因 Maturase | matK |
蛋白酶Protease | clpP1 | |
乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase | accD | |
翻译起始因子 Translation initiation factor | infA | |
包膜蛋白基因 Envelope membrane protein | cemA | |
C型细胞色素合成基因 C-type cytochrome synthesis gene | ccsA | |
未知功能Unknown function | 假定叶绿体阅读框 Hypothetical chloroplast reading frames | ycf1、ycf2(2) |
Table 1 List of genes found in chloroplast genome of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan
基因分类 Category | 基因分组 Gene group | 基因名称 Gene name |
---|---|---|
光合作用 Photosynthesis | 光合系统I基因 Photosystem I | psaA、psaB、psaC、psaI、psaJ |
光合系统II基因 Photosystem II | psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ | |
细胞色素复合物基因 Cytochrome b/f complex | petA、petB、petD、petG、petL、petN | |
ATP合成酶基因 ATP synthase | atpA、atpB、atpE、atpF、atpH、atpI | |
NADH脱氢酶基因 NADH dehydrogenase | ndhA、ndhB(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK | |
二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit | rbcL | |
自我复制Self-replication | RNA聚合酶亚基基因RNA polymeras | rpoA、rpoB、rpoC1、rpoC2 |
核糖体小亚基基因 Ribosomal proteins(SSU) | rps11、rps12(2)、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7(2)、rps8 | |
核糖体大亚基基因 Ribosomal proteins(LSU) | rpl14、rpl16、rpl2(2)、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36、 | |
转运RNA基因 Transfer RNAs | trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU(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-UGU、trnV-GAC(2)、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU | |
核糖体RNA基因 Ribosomal RNAs | rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2) | |
其他基因 Other genes | 成熟酶基因 Maturase | matK |
蛋白酶Protease | clpP1 | |
乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase | accD | |
翻译起始因子 Translation initiation factor | infA | |
包膜蛋白基因 Envelope membrane protein | cemA | |
C型细胞色素合成基因 C-type cytochrome synthesis gene | ccsA | |
未知功能Unknown function | 假定叶绿体阅读框 Hypothetical chloroplast reading frames | ycf1、ycf2(2) |
区域Area | 碱基长度 Base length/ bp | T/% | C/% | A/% | G/% | GC/% | AT偏斜值AT skew | GC 偏斜值GC skew |
---|---|---|---|---|---|---|---|---|
大单拷贝区LSC | 89 814 | 33.58 | 17.59 | 32.04 | 16.79 | 34.38 | -0.023 5 | -0.023 3 |
小单拷贝区SSC | 22 074 | 36.02 | 15.12 | 34.97 | 13.89 | 29.01 | -0.014 8 | -0.042 4 |
反向重复序列a(IRa) | 25 328 | 29.01 | 21.95 | 28.59 | 20.44 | 42.40 | -0.007 3 | -0.035 6 |
反向重复序列b(IRb) | 25 328 | 28.59 | 20.44 | 29.01 | 21.95 | 42.40 | 0.007 3 | 0.035 6 |
总基因组 | 162 544 | 32.42 | 18.38 | 31.43 | 17.77 | 36.15 | -0.015 5 | -0.016 9 |
Table 2 Nucleotide composition of the whole chloroplast genome of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan
区域Area | 碱基长度 Base length/ bp | T/% | C/% | A/% | G/% | GC/% | AT偏斜值AT skew | GC 偏斜值GC skew |
---|---|---|---|---|---|---|---|---|
大单拷贝区LSC | 89 814 | 33.58 | 17.59 | 32.04 | 16.79 | 34.38 | -0.023 5 | -0.023 3 |
小单拷贝区SSC | 22 074 | 36.02 | 15.12 | 34.97 | 13.89 | 29.01 | -0.014 8 | -0.042 4 |
反向重复序列a(IRa) | 25 328 | 29.01 | 21.95 | 28.59 | 20.44 | 42.40 | -0.007 3 | -0.035 6 |
反向重复序列b(IRb) | 25 328 | 28.59 | 20.44 | 29.01 | 21.95 | 42.40 | 0.007 3 | 0.035 6 |
总基因组 | 162 544 | 32.42 | 18.38 | 31.43 | 17.77 | 36.15 | -0.015 5 | -0.016 9 |
核苷酸类型 Nucleotide type | 简单重复序列 Simple sequence repeat | 重复序列个数 Number of SSR |
---|---|---|
单核苷酸 Mononucleotide | A | 45 |
C | 2 | |
G | 1 | |
T | 36 | |
二核苷酸 Dinucleotide | AT | 5 |
TA | 10 | |
三核苷酸 Trinucleotide | TTA | 1 |
四核苷酸 Tetranucleotide | TATG | 1 |
Table 3 Simple sequence repeats(SSR)type of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan
核苷酸类型 Nucleotide type | 简单重复序列 Simple sequence repeat | 重复序列个数 Number of SSR |
---|---|---|
单核苷酸 Mononucleotide | A | 45 |
C | 2 | |
G | 1 | |
T | 36 | |
二核苷酸 Dinucleotide | AT | 5 |
TA | 10 | |
三核苷酸 Trinucleotide | TTA | 1 |
四核苷酸 Tetranucleotide | TATG | 1 |
Fig. 2 IR boundary analysis of the chloroplast genomes of C. cormosus cv. L. Schoot var. Cormosus ‘Hongyayu’ from Jiangxi Yanshan and its 11 related species
Fig. 4 Nucleotide diversity of chloroplast genomes of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan and its 11 related species
基因 Gene | GC含量 GC content/% | 基因 Gene | GC含量 GC content/% | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
平均 GCall | 第一密码子GC1 | 第二密码子GC2 | 第三密码子GC3 | 有效密码子数ENC | 平均 GCall | 第一密码子GC1 | 第二密码子GC2 | 第三密码子GC3 | 有效密码子数ENC | ||||
accD | 34.62 | 38.62 | 37.40 | 27.85 | 44.206 | psbH | 42.34 | 48.65 | 47.30 | 31.08 | 43.164 | ||
atpA | 40.03 | 55.71 | 39.17 | 25.20 | 44.586 | psbI | 36.94 | 48.65 | 29.73 | 32.43 | 40.922 | ||
atpB | 42.48 | 56.91 | 41.68 | 28.86 | 48.495 | psbJ | 41.46 | 41.46 | 53.66 | 29.27 | 20.769 | ||
atpE | 41.67 | 52.94 | 41.91 | 30.15 | 46.888 | psbK | 37.57 | 42.86 | 36.51 | 33.33 | 42.160 | ||
atpF | 37.73 | 50.00 | 35.16 | 28.02 | 39.808 | psbL | 29.06 | 35.90 | 28.21 | 23.08 | 50.514 | ||
atpH | 44.31 | 62.20 | 48.78 | 21.95 | 49.183 | psbM | 28.57 | 42.86 | 25.71 | 17.14 | 31.500 | ||
atpI | 38.04 | 49.19 | 37.90 | 27.02 | 43.152 | psbT | 35.29 | 41.18 | 35.29 | 29.41 | 34.772 | ||
ccsA | 32.1 | 32.10 | 37.96 | 26.23 | 43.768 | psbZ | 34.39 | 38.10 | 42.86 | 22.22 | 51.110 | ||
cemA | 31.45 | 39.62 | 27.04 | 27.67 | 40.639 | rbcL | 43.04 | 57.38 | 43.66 | 28.07 | 47.314 | ||
clpP1 | 42.69 | 59.61 | 36.95 | 31.53 | 59.229 | rpl2 | 43.80 | 50.73 | 49.27 | 31.39 | 50.648 | ||
matK | 31.58 | 38.99 | 31.19 | 24.56 | 46.593 | rpl2 | 43.80 | 50.73 | 49.27 | 31.39 | 50.648 | ||
ndhA | 35.81 | 44.51 | 37.91 | 25.00 | 44.550 | rpl14 | 39.02 | 53.66 | 38.21 | 25.20 | 56.951 | ||
ndhB | 37.77 | 42.07 | 39.53 | 31.70 | 47.366 | rpl16 | 43.87 | 50.74 | 53.68 | 27.21 | 40.180 | ||
ndhB | 37.77 | 42.07 | 39.53 | 31.70 | 47.366 | rpl20 | 36.44 | 37.29 | 44.92 | 27.12 | 43.650 | ||
ndhC | 37.47 | 49.59 | 33.88 | 28.93 | 45.634 | rpl22 | 37.63 | 45.16 | 40.32 | 27.42 | 51.065 | ||
ndhD | 35.46 | 39.72 | 38.52 | 28.14 | 49.596 | rpl23 | 37.04 | 41.11 | 40.00 | 30.00 | 52.839 | ||
ndhE | 31.37 | 38.24 | 33.33 | 22.55 | 42.469 | rpl23 | 37.04 | 41.11 | 40.00 | 30.00 | 52.839 | ||
ndhF | 33.06 | 37.42 | 36.88 | 24.90 | 45.696 | rpl32 | 33.91 | 34.48 | 44.83 | 22.41 | 34.549 | ||
ndhG | 33.15 | 42.37 | 33.33 | 23.73 | 43.846 | rpl33 | 34.33 | 38.81 | 38.81 | 25.37 | 42.754 | ||
ndhH | 38.16 | 51.78 | 35.79 | 26.90 | 48.229 | rpl36 | 37.72 | 42.11 | 47.37 | 23.68 | 46.750 | ||
ndhI | 34.44 | 43.89 | 36.67 | 22.78 | 44.213 | rpoA | 35.00 | 45.59 | 34.41 | 25.00 | 49.552 | ||
ndhJ | 39.2 | 48.43 | 37.74 | 31.45 | 51.139 | rpoB | 39.05 | 50.23 | 37.74 | 29.17 | 49.169 | ||
ndhK | 38.82 | 43.37 | 43.37 | 29.72 | 51.528 | rpoC1 | 38.40 | 50.29 | 38.16 | 26.75 | 49.009 | ||
pafI | 39.45 | 47.34 | 40.83 | 30.18 | 55.939 | rpoC2 | 37.48 | 46.02 | 37.63 | 28.80 | 50.022 | ||
pafII | 38.92 | 44.86 | 40.54 | 31.35 | 51.331 | rps2 | 38.96 | 43.88 | 43.04 | 29.96 | 45.542 | ||
pbf1 | 46.21 | 52.27 | 43.18 | 43.18 | 48.475 | rps3 | 34.86 | 46.58 | 34.25 | 23.74 | 45.101 | ||
petA | 40.5 | 53.58 | 35.51 | 32.4 | 51.521 | rps4 | 37.79 | 49.01 | 38.12 | 26.24 | 50.288 | ||
petB | 39.66 | 47.22 | 41.67 | 30.09 | 42.013 | rps7 | 39.10 | 52.56 | 44.87 | 19.87 | 44.746 | ||
petD | 38.72 | 50.93 | 39.13 | 26.09 | 44.396 | rps7 | 39.10 | 52.56 | 44.87 | 19.87 | 44.746 | ||
petG | 38.6 | 55.26 | 31.58 | 28.95 | 33.100 | rps8 | 36.09 | 41.35 | 42.11 | 24.81 | 42.540 | ||
petL | 37.5 | 37.50 | 46.88 | 28.12 | 35.182 | rps11 | 44.12 | 55.40 | 57.55 | 19.42 | 41.507 | ||
petN | 41.11 | 50.00 | 43.33 | 30.00 | 30.698 | rps12 | 41.94 | 52.42 | 48.39 | 25.00 | 43.732 | ||
psaA | 43.01 | 51.93 | 43.68 | 33.42 | 49.161 | rps12 | 41.94 | 52.42 | 48.39 | 25.00 | 43.732 | ||
psaB | 40.91 | 48.44 | 42.99 | 31.29 | 48.022 | rps14 | 41.58 | 42.57 | 46.53 | 35.64 | 37.716 | ||
psaC | 43.9 | 43.90 | 53.66 | 34.15 | 48.358 | rps15 | 34.05 | 40.86 | 29.03 | 32.26 | 49.599 | ||
psaI | 35.14 | 43.24 | 27.03 | 35.14 | 44.365 | rps16 | 35.86 | 50.63 | 36.71 | 20.25 | 42.450 | ||
psaJ | 35.66 | 41.86 | 39.53 | 25.58 | 42.629 | rps18 | 34.31 | 35.29 | 44.12 | 23.53 | 37.936 | ||
psbA | 42.66 | 49.72 | 43.79 | 34.46 | 41.107 | rps19 | 35.84 | 43.01 | 39.78 | 24.73 | 42.905 | ||
psbB | 43.42 | 54.42 | 46.37 | 29.47 | 48.296 | ycf1 | 30.85 | 37.27 | 30.03 | 25.25 | 47.451 | ||
psbC | 44.37 | 54.33 | 46.54 | 32.25 | 45.499 | ycf2 | 37.43 | 41.19 | 34.60 | 36.51 | 52.960 | ||
psbD | 42.18 | 51.98 | 43.50 | 31.07 | 44.142 | ycf2 | 37.43 | 41.19 | 34.60 | 36.51 | 52.960 | ||
psbE | 40.08 | 42.86 | 46.43 | 30.95 | 48.400 | 平均 | 38.17 | 46.21 | 40.21 | 28.10 | 45.600 | ||
psbF | 40.83 | 47.50 | 45.00 | 30.00 | 61.000 | Mean |
Table 4 GC content and ENC of 48 CDS codons from the chloroplast of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ in Jiangxi Yanshan
基因 Gene | GC含量 GC content/% | 基因 Gene | GC含量 GC content/% | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
平均 GCall | 第一密码子GC1 | 第二密码子GC2 | 第三密码子GC3 | 有效密码子数ENC | 平均 GCall | 第一密码子GC1 | 第二密码子GC2 | 第三密码子GC3 | 有效密码子数ENC | ||||
accD | 34.62 | 38.62 | 37.40 | 27.85 | 44.206 | psbH | 42.34 | 48.65 | 47.30 | 31.08 | 43.164 | ||
atpA | 40.03 | 55.71 | 39.17 | 25.20 | 44.586 | psbI | 36.94 | 48.65 | 29.73 | 32.43 | 40.922 | ||
atpB | 42.48 | 56.91 | 41.68 | 28.86 | 48.495 | psbJ | 41.46 | 41.46 | 53.66 | 29.27 | 20.769 | ||
atpE | 41.67 | 52.94 | 41.91 | 30.15 | 46.888 | psbK | 37.57 | 42.86 | 36.51 | 33.33 | 42.160 | ||
atpF | 37.73 | 50.00 | 35.16 | 28.02 | 39.808 | psbL | 29.06 | 35.90 | 28.21 | 23.08 | 50.514 | ||
atpH | 44.31 | 62.20 | 48.78 | 21.95 | 49.183 | psbM | 28.57 | 42.86 | 25.71 | 17.14 | 31.500 | ||
atpI | 38.04 | 49.19 | 37.90 | 27.02 | 43.152 | psbT | 35.29 | 41.18 | 35.29 | 29.41 | 34.772 | ||
ccsA | 32.1 | 32.10 | 37.96 | 26.23 | 43.768 | psbZ | 34.39 | 38.10 | 42.86 | 22.22 | 51.110 | ||
cemA | 31.45 | 39.62 | 27.04 | 27.67 | 40.639 | rbcL | 43.04 | 57.38 | 43.66 | 28.07 | 47.314 | ||
clpP1 | 42.69 | 59.61 | 36.95 | 31.53 | 59.229 | rpl2 | 43.80 | 50.73 | 49.27 | 31.39 | 50.648 | ||
matK | 31.58 | 38.99 | 31.19 | 24.56 | 46.593 | rpl2 | 43.80 | 50.73 | 49.27 | 31.39 | 50.648 | ||
ndhA | 35.81 | 44.51 | 37.91 | 25.00 | 44.550 | rpl14 | 39.02 | 53.66 | 38.21 | 25.20 | 56.951 | ||
ndhB | 37.77 | 42.07 | 39.53 | 31.70 | 47.366 | rpl16 | 43.87 | 50.74 | 53.68 | 27.21 | 40.180 | ||
ndhB | 37.77 | 42.07 | 39.53 | 31.70 | 47.366 | rpl20 | 36.44 | 37.29 | 44.92 | 27.12 | 43.650 | ||
ndhC | 37.47 | 49.59 | 33.88 | 28.93 | 45.634 | rpl22 | 37.63 | 45.16 | 40.32 | 27.42 | 51.065 | ||
ndhD | 35.46 | 39.72 | 38.52 | 28.14 | 49.596 | rpl23 | 37.04 | 41.11 | 40.00 | 30.00 | 52.839 | ||
ndhE | 31.37 | 38.24 | 33.33 | 22.55 | 42.469 | rpl23 | 37.04 | 41.11 | 40.00 | 30.00 | 52.839 | ||
ndhF | 33.06 | 37.42 | 36.88 | 24.90 | 45.696 | rpl32 | 33.91 | 34.48 | 44.83 | 22.41 | 34.549 | ||
ndhG | 33.15 | 42.37 | 33.33 | 23.73 | 43.846 | rpl33 | 34.33 | 38.81 | 38.81 | 25.37 | 42.754 | ||
ndhH | 38.16 | 51.78 | 35.79 | 26.90 | 48.229 | rpl36 | 37.72 | 42.11 | 47.37 | 23.68 | 46.750 | ||
ndhI | 34.44 | 43.89 | 36.67 | 22.78 | 44.213 | rpoA | 35.00 | 45.59 | 34.41 | 25.00 | 49.552 | ||
ndhJ | 39.2 | 48.43 | 37.74 | 31.45 | 51.139 | rpoB | 39.05 | 50.23 | 37.74 | 29.17 | 49.169 | ||
ndhK | 38.82 | 43.37 | 43.37 | 29.72 | 51.528 | rpoC1 | 38.40 | 50.29 | 38.16 | 26.75 | 49.009 | ||
pafI | 39.45 | 47.34 | 40.83 | 30.18 | 55.939 | rpoC2 | 37.48 | 46.02 | 37.63 | 28.80 | 50.022 | ||
pafII | 38.92 | 44.86 | 40.54 | 31.35 | 51.331 | rps2 | 38.96 | 43.88 | 43.04 | 29.96 | 45.542 | ||
pbf1 | 46.21 | 52.27 | 43.18 | 43.18 | 48.475 | rps3 | 34.86 | 46.58 | 34.25 | 23.74 | 45.101 | ||
petA | 40.5 | 53.58 | 35.51 | 32.4 | 51.521 | rps4 | 37.79 | 49.01 | 38.12 | 26.24 | 50.288 | ||
petB | 39.66 | 47.22 | 41.67 | 30.09 | 42.013 | rps7 | 39.10 | 52.56 | 44.87 | 19.87 | 44.746 | ||
petD | 38.72 | 50.93 | 39.13 | 26.09 | 44.396 | rps7 | 39.10 | 52.56 | 44.87 | 19.87 | 44.746 | ||
petG | 38.6 | 55.26 | 31.58 | 28.95 | 33.100 | rps8 | 36.09 | 41.35 | 42.11 | 24.81 | 42.540 | ||
petL | 37.5 | 37.50 | 46.88 | 28.12 | 35.182 | rps11 | 44.12 | 55.40 | 57.55 | 19.42 | 41.507 | ||
petN | 41.11 | 50.00 | 43.33 | 30.00 | 30.698 | rps12 | 41.94 | 52.42 | 48.39 | 25.00 | 43.732 | ||
psaA | 43.01 | 51.93 | 43.68 | 33.42 | 49.161 | rps12 | 41.94 | 52.42 | 48.39 | 25.00 | 43.732 | ||
psaB | 40.91 | 48.44 | 42.99 | 31.29 | 48.022 | rps14 | 41.58 | 42.57 | 46.53 | 35.64 | 37.716 | ||
psaC | 43.9 | 43.90 | 53.66 | 34.15 | 48.358 | rps15 | 34.05 | 40.86 | 29.03 | 32.26 | 49.599 | ||
psaI | 35.14 | 43.24 | 27.03 | 35.14 | 44.365 | rps16 | 35.86 | 50.63 | 36.71 | 20.25 | 42.450 | ||
psaJ | 35.66 | 41.86 | 39.53 | 25.58 | 42.629 | rps18 | 34.31 | 35.29 | 44.12 | 23.53 | 37.936 | ||
psbA | 42.66 | 49.72 | 43.79 | 34.46 | 41.107 | rps19 | 35.84 | 43.01 | 39.78 | 24.73 | 42.905 | ||
psbB | 43.42 | 54.42 | 46.37 | 29.47 | 48.296 | ycf1 | 30.85 | 37.27 | 30.03 | 25.25 | 47.451 | ||
psbC | 44.37 | 54.33 | 46.54 | 32.25 | 45.499 | ycf2 | 37.43 | 41.19 | 34.60 | 36.51 | 52.960 | ||
psbD | 42.18 | 51.98 | 43.50 | 31.07 | 44.142 | ycf2 | 37.43 | 41.19 | 34.60 | 36.51 | 52.960 | ||
psbE | 40.08 | 42.86 | 46.43 | 30.95 | 48.400 | 平均 | 38.17 | 46.21 | 40.21 | 28.10 | 45.600 | ||
psbF | 40.83 | 47.50 | 45.00 | 30.00 | 61.000 | Mean |
氨基酸 Amino acid | 密码子 Codon | 数量 Amount | 相对使用度RSCU | 氨基酸 Amino acid | 密码子 Codon | 数量 Amount | 相对使用度RSCU | ||
---|---|---|---|---|---|---|---|---|---|
丙氨酸 Ala | GCA | 420 | 1.187 28 | 赖氨酸 Lys | AAA | 1 036 | 1.48 318 | ||
GCC | 215 | 0.607 774 | AAG | 361 | 0.516 822 | ||||
GCG | 145 | 0.409 894 | 蛋氨酸Met | AUG | 596 | 1.993 31 | |||
GCU | 635 | 1.795 05 | GUG | 2 | 0.006 688 96 | ||||
精氨酸 Arg | AGA | 521 | 1.953 75 | 苯丙氨酸Phe | UUC | 536 | 0.724 324 | ||
AGG | 154 | 0.577 5 | UUU | 944 | 1.275 68 | ||||
CGA | 358 | 1.342 5 | 脯氨酸 Pro | CCA | 322 | 1.194 81 | |||
CGC | 96 | 0.36 | CCC | 197 | 0.730 983 | ||||
CGG | 113 | 0.423 75 | CCG | 123 | 0.456 401 | ||||
CGU | 358 | 1.342 5 | CCU | 436 | 1.617 81 | ||||
天冬酰胺 Asn | AAC | 290 | 0.464 | 丝氨酸 Ser | AGC | 104 | 0.298 851 | ||
AAU | 960 | 1.536 | AGU | 447 | 1.284 48 | ||||
天冬氨酸 Asp | GAC | 213 | 0.394 81 | UCA | 444 | 1.275 86 | |||
GAU | 866 | 1.605 19 | UCC | 339 | 0.974 138 | ||||
半胱氨酸 Cys | UGC | 74 | 0.485 246 | UCG | 179 | 0.514 368 | |||
UGU | 231 | 1.514 75 | UCU | 575 | 1.652 3 | ||||
谷氨酰胺 Gln | CAA | 690 | 1.490 28 | 终止密码子Ter | UAA | 38 | 1.357 14 | ||
CAG | 236 | 0.509 719 | UAG | 26 | 0.928 571 | ||||
谷氨酸 Glu | GAA | 1 035 | 1.483 87 | UGA | 20 | 0.714 286 | |||
GAG | 360 | 0.516 129 | 苏氨酸 Thr | ACA | 433 | 1.277 29 | |||
甘氨酸 Gly | GGA | 719 | 1.632 24 | ACC | 247 | 0.728 614 | |||
GGC | 161 | 0.365 494 | ACG | 149 | 0.439 528 | ||||
GGG | 305 | 0.692 395 | ACU | 527 | 1.554 57 | ||||
GGU | 577 | 1.309 88 | 色氨酸Trp | UGG | 443 | 1 | |||
组氨酸 His | CAC | 153 | 0.485 714 | 酪氨酸 Tyr | UAC | 208 | 0.428 424 | ||
CAU | 477 | 1.514 29 | UAU | 763 | 1.571 58 | ||||
异亮氨酸 Ile | AUA | 702 | 0.950 79 | 缬氨酸 Val | GUA | 542 | 1.503 47 | ||
AUC | 424 | 0.574 266 | GUC | 186 | 0.515 95 | ||||
AUU | 1 089 | 1.474 94 | GUG | 194 | 0.538 141 | ||||
亮氨酸 Leu | CUA | 358 | 0.792 62 | GUU | 520 | 1.442 44 | |||
CUC | 186 | 0.411 808 | |||||||
CUG | 163 | 0.360 886 | |||||||
CUU | 584 | 1.292 99 | |||||||
UUA | 834 | 1.846 49 | |||||||
UUG | 585 | 1.295 2 |
Table 5 RSCU analysis of amino acid codons in the chloroplast genome of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan
氨基酸 Amino acid | 密码子 Codon | 数量 Amount | 相对使用度RSCU | 氨基酸 Amino acid | 密码子 Codon | 数量 Amount | 相对使用度RSCU | ||
---|---|---|---|---|---|---|---|---|---|
丙氨酸 Ala | GCA | 420 | 1.187 28 | 赖氨酸 Lys | AAA | 1 036 | 1.48 318 | ||
GCC | 215 | 0.607 774 | AAG | 361 | 0.516 822 | ||||
GCG | 145 | 0.409 894 | 蛋氨酸Met | AUG | 596 | 1.993 31 | |||
GCU | 635 | 1.795 05 | GUG | 2 | 0.006 688 96 | ||||
精氨酸 Arg | AGA | 521 | 1.953 75 | 苯丙氨酸Phe | UUC | 536 | 0.724 324 | ||
AGG | 154 | 0.577 5 | UUU | 944 | 1.275 68 | ||||
CGA | 358 | 1.342 5 | 脯氨酸 Pro | CCA | 322 | 1.194 81 | |||
CGC | 96 | 0.36 | CCC | 197 | 0.730 983 | ||||
CGG | 113 | 0.423 75 | CCG | 123 | 0.456 401 | ||||
CGU | 358 | 1.342 5 | CCU | 436 | 1.617 81 | ||||
天冬酰胺 Asn | AAC | 290 | 0.464 | 丝氨酸 Ser | AGC | 104 | 0.298 851 | ||
AAU | 960 | 1.536 | AGU | 447 | 1.284 48 | ||||
天冬氨酸 Asp | GAC | 213 | 0.394 81 | UCA | 444 | 1.275 86 | |||
GAU | 866 | 1.605 19 | UCC | 339 | 0.974 138 | ||||
半胱氨酸 Cys | UGC | 74 | 0.485 246 | UCG | 179 | 0.514 368 | |||
UGU | 231 | 1.514 75 | UCU | 575 | 1.652 3 | ||||
谷氨酰胺 Gln | CAA | 690 | 1.490 28 | 终止密码子Ter | UAA | 38 | 1.357 14 | ||
CAG | 236 | 0.509 719 | UAG | 26 | 0.928 571 | ||||
谷氨酸 Glu | GAA | 1 035 | 1.483 87 | UGA | 20 | 0.714 286 | |||
GAG | 360 | 0.516 129 | 苏氨酸 Thr | ACA | 433 | 1.277 29 | |||
甘氨酸 Gly | GGA | 719 | 1.632 24 | ACC | 247 | 0.728 614 | |||
GGC | 161 | 0.365 494 | ACG | 149 | 0.439 528 | ||||
GGG | 305 | 0.692 395 | ACU | 527 | 1.554 57 | ||||
GGU | 577 | 1.309 88 | 色氨酸Trp | UGG | 443 | 1 | |||
组氨酸 His | CAC | 153 | 0.485 714 | 酪氨酸 Tyr | UAC | 208 | 0.428 424 | ||
CAU | 477 | 1.514 29 | UAU | 763 | 1.571 58 | ||||
异亮氨酸 Ile | AUA | 702 | 0.950 79 | 缬氨酸 Val | GUA | 542 | 1.503 47 | ||
AUC | 424 | 0.574 266 | GUC | 186 | 0.515 95 | ||||
AUU | 1 089 | 1.474 94 | GUG | 194 | 0.538 141 | ||||
亮氨酸 Leu | CUA | 358 | 0.792 62 | GUU | 520 | 1.442 44 | |||
CUC | 186 | 0.411 808 | |||||||
CUG | 163 | 0.360 886 | |||||||
CUU | 584 | 1.292 99 | |||||||
UUA | 834 | 1.846 49 | |||||||
UUG | 585 | 1.295 2 |
Fig. 7 Neutrality plot analysis of chloroplast genes of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan and its 11 related species A-L successively represents 11 related species(C. esculenta JN105690, C. esculenta NC_016753, R. vivipara MT884912, S. sp. 0020020418 MT884849, S. colocasiifolia NC_051952, A. peltata MT884904, A. fornicata MK636779, A. navicularis MN046882, L. gigantea NC_060475, E. hypnosum MT884866, A. cucullata NC_060696). The same below
氨基酸 Amino acid | 密码子 Codon | 低表达基因 Low expressed gene | 高表达基因 High expressed gene | 相对使用度差值 △RSCU | |||
---|---|---|---|---|---|---|---|
相对使用度 RSCU | 数量 Amount | 相对使用度 RSCU | 数量 Amount | ||||
Ala | GCU | 1.854 3 | 70 | 2 | 8 | 0.145 7 | |
Arg | CGU | 0.672 414 | 39 | 1.875 | 3 | 1.202 586 | |
AGG | 0.879 31 | 51 | 1.25 | 2 | 0.370 69 | ||
CGC | 0.379 31 | 22 | 0.625 | 1 | 0.245 69 | ||
Asn | AAC | 0.520 376 | 83 | 1 | 3 | 0.479 624 | |
Gln | CAA | 1.299 49 | 128 | 1.5 | 3 | 0.200 51 | |
Gly | GGU | 0.967 442 | 52 | 1.312 5 | 7 | 0.345 058 | |
Ile | AUU | 1.334 93 | 186 | 2 | 12 | 0.665 07 | |
Leu | UUA | 1.043 48 | 92 | 1.555 56 | 7 | 0.512 08 | |
CUU | 1.417 77 | 125 | 1.555 56 | 7 | 0.137 79 | ||
CUA | 0.793 951 | 70 | 1.111 11 | 5 | 0.317 159 | ||
Lys | AAA | 1.254 78 | 197 | 1.538 46 | 10 | 0.283 68 | |
Phe | UUU | 1.032 84 | 173 | 1.666 67 | 10 | 0.633 83 | |
Pro | CCU | 1.301 44 | 68 | 1.6 | 4 | 0.298 56 | |
Ser | AGU | 0.928 433 | 80 | 1.263 16 | 6 | 0.334 727 | |
UCA | 1.334 62 | 115 | 1.473 68 | 7 | 0.139 06 | ||
Ter | UGA | 0 | 0 | 0.6 | 1 | 0.6 | |
UAG | 0.666 667 | 2 | 1.2 | 2 | 0.533 333 | ||
Thr | ACU | 1.192 66 | 65 | 1.384 62 | 9 | 0.191 96 | |
Tyr | UAC | 0.402 174 | 37 | 0.666 667 | 2 | 0.264 493 | |
Val | GUA | 1.106 8 | 57 | 2.117 65 | 9 | 1.010 85 |
Table 6 Putative optimal codons in chloroplast genome of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan
氨基酸 Amino acid | 密码子 Codon | 低表达基因 Low expressed gene | 高表达基因 High expressed gene | 相对使用度差值 △RSCU | |||
---|---|---|---|---|---|---|---|
相对使用度 RSCU | 数量 Amount | 相对使用度 RSCU | 数量 Amount | ||||
Ala | GCU | 1.854 3 | 70 | 2 | 8 | 0.145 7 | |
Arg | CGU | 0.672 414 | 39 | 1.875 | 3 | 1.202 586 | |
AGG | 0.879 31 | 51 | 1.25 | 2 | 0.370 69 | ||
CGC | 0.379 31 | 22 | 0.625 | 1 | 0.245 69 | ||
Asn | AAC | 0.520 376 | 83 | 1 | 3 | 0.479 624 | |
Gln | CAA | 1.299 49 | 128 | 1.5 | 3 | 0.200 51 | |
Gly | GGU | 0.967 442 | 52 | 1.312 5 | 7 | 0.345 058 | |
Ile | AUU | 1.334 93 | 186 | 2 | 12 | 0.665 07 | |
Leu | UUA | 1.043 48 | 92 | 1.555 56 | 7 | 0.512 08 | |
CUU | 1.417 77 | 125 | 1.555 56 | 7 | 0.137 79 | ||
CUA | 0.793 951 | 70 | 1.111 11 | 5 | 0.317 159 | ||
Lys | AAA | 1.254 78 | 197 | 1.538 46 | 10 | 0.283 68 | |
Phe | UUU | 1.032 84 | 173 | 1.666 67 | 10 | 0.633 83 | |
Pro | CCU | 1.301 44 | 68 | 1.6 | 4 | 0.298 56 | |
Ser | AGU | 0.928 433 | 80 | 1.263 16 | 6 | 0.334 727 | |
UCA | 1.334 62 | 115 | 1.473 68 | 7 | 0.139 06 | ||
Ter | UGA | 0 | 0 | 0.6 | 1 | 0.6 | |
UAG | 0.666 667 | 2 | 1.2 | 2 | 0.533 333 | ||
Thr | ACU | 1.192 66 | 65 | 1.384 62 | 9 | 0.191 96 | |
Tyr | UAC | 0.402 174 | 37 | 0.666 667 | 2 | 0.264 493 | |
Val | GUA | 1.106 8 | 57 | 2.117 65 | 9 | 1.010 85 |
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