草业学报 ›› 2023, Vol. 32 ›› Issue (7): 85-95.DOI: 10.11686/cyxb2022332
收稿日期:
2022-08-17
修回日期:
2022-11-04
出版日期:
2023-07-20
发布日期:
2023-05-26
通讯作者:
李钰莹,董宽虎
作者简介:
E-mail: dongkuanhu@sxau.edu.cn基金资助:
Shou-yu GAO(), Yu-ying LI(), Zhi-qing YANG, Kuan-hu DONG(), Fang-shan XIA
Received:
2022-08-17
Revised:
2022-11-04
Online:
2023-07-20
Published:
2023-05-26
Contact:
Yu-ying LI,Kuan-hu DONG
摘要:
叶绿体基因组具有高度的保守性和较慢的进化速率,研究叶绿体基因组密码子偏好性可以明确基因表达效率,确定植物系统发育和物种进化。为解析白羊草及其近缘种的系统发育关系,利用CAIcal和CodonW 1.4.2等软件分析了白羊草的叶绿体基因组密码子使用模式,并利用白羊草及其近缘种的同义密码子相对使用度(RSCU)数据构建了聚类图。结果显示:经筛选后的白羊草叶绿体基因组序列中GC的平均含量为38.79%,其中GC1>GC2>GC3;密码子第3位碱基多为A或U;有效密码子数(ENC)的取值为36~61,密码子偏好性较弱;高频率使用的密码子共计26个,其中25个高频密码子以A或U结尾。结合中性绘图、ENC-plot、ENC比值和PR2-plot分析,结果表明白羊草叶绿体基因的密码子偏好性同时受到突变压力和自然选择的影响,且突变压力的影响较大。RSCU数据分析共筛选出15个最优密码子,均以A或U结尾。RSCU聚类结果显示白羊草在密码子使用模式上与近缘物种有所不同。本结果可为孔颖草属植物系统发育研究提供参考。
高守舆, 李钰莹, 杨志青, 董宽虎, 夏方山. 白羊草叶绿体基因组密码子使用偏好性分析[J]. 草业学报, 2023, 32(7): 85-95.
Shou-yu GAO, Yu-ying LI, Zhi-qing YANG, Kuan-hu DONG, Fang-shan XIA. Codon usage bias analysis of the chloroplast genome of Bothriochloa ischaemum[J]. Acta Prataculturae Sinica, 2023, 32(7): 85-95.
指标 Index | GCall | GC1 | GC2 | GC3 | GC3s |
---|---|---|---|---|---|
GC1 | 0.7894** | ||||
GC2 | 0.6752** | 0.2725 | |||
GC3 | 0.5759** | 0.2749 | 0.0549 | ||
GC3s | 0.5418** | 0.2699 | 0.0305 | 0.9516** | |
ENC | -0.0177 | 0.0394 | -0.3996** | 0.4138** | 0.4866** |
表1 白羊草碱基组成与密码子使用偏好相关性
Table 1 Correlation between base composition and codon usage bias of B. ischaemum
指标 Index | GCall | GC1 | GC2 | GC3 | GC3s |
---|---|---|---|---|---|
GC1 | 0.7894** | ||||
GC2 | 0.6752** | 0.2725 | |||
GC3 | 0.5759** | 0.2749 | 0.0549 | ||
GC3s | 0.5418** | 0.2699 | 0.0305 | 0.9516** | |
ENC | -0.0177 | 0.0394 | -0.3996** | 0.4138** | 0.4866** |
组限 Class limits | 组中值 Class midvalue | 组数 Frequency number | 组频 Frequency (%) |
---|---|---|---|
-0.25~-0.15 | -0.20 | 3 | 5.88 |
-0.15~-0.05 | -0.10 | 10 | 19.61 |
-0.05~0.05 | 0.00 | 30 | 58.82 |
0.05~0.15 | 0.10 | 6 | 11.76 |
0.15~0.25 | 0.20 | 2 | 3.92 |
合计Total | 51 | 1.00 |
表2 ENC比值分布
Table 2 Distribution of ENC ration
组限 Class limits | 组中值 Class midvalue | 组数 Frequency number | 组频 Frequency (%) |
---|---|---|---|
-0.25~-0.15 | -0.20 | 3 | 5.88 |
-0.15~-0.05 | -0.10 | 10 | 19.61 |
-0.05~0.05 | 0.00 | 30 | 58.82 |
0.05~0.15 | 0.10 | 6 | 11.76 |
0.15~0.25 | 0.20 | 2 | 3.92 |
合计Total | 51 | 1.00 |
氨基酸 Amino acid | 密码子 Codon | RSCU | 低RSCU Low RSCU | 高RSCU High RSCU | △RSCU | 氨基酸 Amino acid | 密码子 Codon | RSCU | 低RSCU Low RSCU | 高RSCU High RSCU | △RSCU |
---|---|---|---|---|---|---|---|---|---|---|---|
苯丙氨酸Phe | 1.31 | 1.14 | 1.22 | 0.08 | 丙氨酸Ala | 1.80 | 1.74 | 2.11 | 0.37 | ||
UUC | 0.69 | 0.86 | 0.78 | -0.08 | GCC | 0.61 | 0.87 | 0.27 | -0.60 | ||
亮氨酸Leu | 2.03 | 1.32 | 2.50 | 1.18 | GCA* | 1.16 | 0.78 | 1.35 | 0.57 | ||
UUG | 1.09 | 1.17 | 0.80 | -0.37 | GCG | 0.44 | 0.61 | 0.27 | -0.34 | ||
CUU | 1.32 | 1.98 | 1.18 | -0.80 | 酪氨酸Tyr | UAU | 1.59 | 1.50 | 1.57 | 0.07 | |
CUC* | 0.37 | 0.07 | 0.28 | 0.21 | UAC | 0.41 | 0.50 | 0.43 | -0.07 | ||
CUA | 0.86 | 1.24 | 0.94 | -0.30 | 组氨酸His | CAU | 1.46 | 1.44 | 0.94 | -0.50 | |
CUG | 0.32 | 0.22 | 0.28 | 0.06 | CAC* | 0.54 | 0.56 | 1.06 | 0.50 | ||
异亮氨酸Ile | AUU | 1.50 | 1.46 | 1.41 | -0.05 | 谷氨酰胺Gln | CAA | 1.52 | 1.48 | 1.46 | -0.02 |
AUC* | 0.55 | 0.41 | 0.58 | 0.17 | CAG | 0.48 | 0.52 | 0.54 | 0.02 | ||
AUA | 0.95 | 1.13 | 1.01 | -0.12 | 天冬酰胺Asn | AAU | 1.50 | 1.52 | 1.18 | -0.34 | |
缬氨酸Val | 1.55 | 1.12 | 1.92 | 0.80 | AAC* | 0.50 | 0.48 | 0.82 | 0.34 | ||
GUC | 0.46 | 0.64 | 0.08 | -0.56 | 赖氨酸Lys | 1.47 | 1.21 | 1.64 | 0.43 | ||
1.49 | 1.60 | 1.77 | 0.17 | AAG | 0.53 | 0.79 | 0.36 | -0.43 | |||
GUG | 0.51 | 0.64 | 0.23 | -0.41 | 天冬氨酸Asp | GAU | 1.57 | 1.76 | 1.68 | -0.08 | |
丝氨酸Ser | 1.62 | 1.25 | 2.02 | 0.77 | GAC* | 0.43 | 0.24 | 0.32 | 0.08 | ||
UCC | 1.21 | 1.50 | 1.43 | -0.07 | 谷氨酸Glu | GAA | 1.51 | 1.71 | 1.42 | -0.29 | |
UCA | 0.99 | 0.75 | 0.48 | -0.27 | GAG* | 0.49 | 0.29 | 0.58 | 0.29 | ||
UCG | 0.53 | 0.92 | 0.24 | -0.68 | 半胱氨酸Cys | 1.47 | 1.69 | 1.78 | 0.09 | ||
1.22 | 1.08 | 1.37 | 0.29 | UGC | 0.53 | 0.31 | 0.22 | -0.09 | |||
AGC | 0.42 | 0.50 | 0.48 | -0.02 | 精氨酸Arg | 1.41 | 1.06 | 2.00 | 0.94 | ||
脯氨酸Pro | 1.53 | 1.04 | 2.00 | 0.96 | CGC | 0.52 | 0.87 | 0.29 | -0.58 | ||
CCC | 0.97 | 1.33 | 1.00 | -0.33 | 1.31 | 1.06 | 1.43 | 0.37 | |||
CCA | 1.05 | 0.74 | 0.77 | 0.03 | CGG | 0.43 | 0.58 | 0.07 | -0.51 | ||
CCG | 0.45 | 0.89 | 0.23 | -0.66 | 1.72 | 1.65 | 1.86 | 0.21 | |||
苏氨酸Thr | 1.67 | 1.18 | 2.00 | 0.82 | AGG | 0.61 | 0.77 | 0.36 | -0.41 | ||
ACC | 0.75 | 0.71 | 0.78 | 0.07 | 甘氨酸Gly | 1.25 | 1.13 | 2.00 | 0.87 | ||
ACA | 1.10 | 1.25 | 1.22 | -0.03 | GGC | 0.45 | 0.35 | 0.45 | 0.10 | ||
ACG | 0.49 | 0.86 | 0.00 | -0.86 | GGA | 1.60 | 1.74 | 1.35 | -0.39 | ||
GGG | 0.70 | 0.78 | 0.20 | -0.58 |
表3 白羊草叶绿体基因组氨基酸相对同义密码子使用度
Table 3 The RSCU of codons in B. ischaemum plastome
氨基酸 Amino acid | 密码子 Codon | RSCU | 低RSCU Low RSCU | 高RSCU High RSCU | △RSCU | 氨基酸 Amino acid | 密码子 Codon | RSCU | 低RSCU Low RSCU | 高RSCU High RSCU | △RSCU |
---|---|---|---|---|---|---|---|---|---|---|---|
苯丙氨酸Phe | 1.31 | 1.14 | 1.22 | 0.08 | 丙氨酸Ala | 1.80 | 1.74 | 2.11 | 0.37 | ||
UUC | 0.69 | 0.86 | 0.78 | -0.08 | GCC | 0.61 | 0.87 | 0.27 | -0.60 | ||
亮氨酸Leu | 2.03 | 1.32 | 2.50 | 1.18 | GCA* | 1.16 | 0.78 | 1.35 | 0.57 | ||
UUG | 1.09 | 1.17 | 0.80 | -0.37 | GCG | 0.44 | 0.61 | 0.27 | -0.34 | ||
CUU | 1.32 | 1.98 | 1.18 | -0.80 | 酪氨酸Tyr | UAU | 1.59 | 1.50 | 1.57 | 0.07 | |
CUC* | 0.37 | 0.07 | 0.28 | 0.21 | UAC | 0.41 | 0.50 | 0.43 | -0.07 | ||
CUA | 0.86 | 1.24 | 0.94 | -0.30 | 组氨酸His | CAU | 1.46 | 1.44 | 0.94 | -0.50 | |
CUG | 0.32 | 0.22 | 0.28 | 0.06 | CAC* | 0.54 | 0.56 | 1.06 | 0.50 | ||
异亮氨酸Ile | AUU | 1.50 | 1.46 | 1.41 | -0.05 | 谷氨酰胺Gln | CAA | 1.52 | 1.48 | 1.46 | -0.02 |
AUC* | 0.55 | 0.41 | 0.58 | 0.17 | CAG | 0.48 | 0.52 | 0.54 | 0.02 | ||
AUA | 0.95 | 1.13 | 1.01 | -0.12 | 天冬酰胺Asn | AAU | 1.50 | 1.52 | 1.18 | -0.34 | |
缬氨酸Val | 1.55 | 1.12 | 1.92 | 0.80 | AAC* | 0.50 | 0.48 | 0.82 | 0.34 | ||
GUC | 0.46 | 0.64 | 0.08 | -0.56 | 赖氨酸Lys | 1.47 | 1.21 | 1.64 | 0.43 | ||
1.49 | 1.60 | 1.77 | 0.17 | AAG | 0.53 | 0.79 | 0.36 | -0.43 | |||
GUG | 0.51 | 0.64 | 0.23 | -0.41 | 天冬氨酸Asp | GAU | 1.57 | 1.76 | 1.68 | -0.08 | |
丝氨酸Ser | 1.62 | 1.25 | 2.02 | 0.77 | GAC* | 0.43 | 0.24 | 0.32 | 0.08 | ||
UCC | 1.21 | 1.50 | 1.43 | -0.07 | 谷氨酸Glu | GAA | 1.51 | 1.71 | 1.42 | -0.29 | |
UCA | 0.99 | 0.75 | 0.48 | -0.27 | GAG* | 0.49 | 0.29 | 0.58 | 0.29 | ||
UCG | 0.53 | 0.92 | 0.24 | -0.68 | 半胱氨酸Cys | 1.47 | 1.69 | 1.78 | 0.09 | ||
1.22 | 1.08 | 1.37 | 0.29 | UGC | 0.53 | 0.31 | 0.22 | -0.09 | |||
AGC | 0.42 | 0.50 | 0.48 | -0.02 | 精氨酸Arg | 1.41 | 1.06 | 2.00 | 0.94 | ||
脯氨酸Pro | 1.53 | 1.04 | 2.00 | 0.96 | CGC | 0.52 | 0.87 | 0.29 | -0.58 | ||
CCC | 0.97 | 1.33 | 1.00 | -0.33 | 1.31 | 1.06 | 1.43 | 0.37 | |||
CCA | 1.05 | 0.74 | 0.77 | 0.03 | CGG | 0.43 | 0.58 | 0.07 | -0.51 | ||
CCG | 0.45 | 0.89 | 0.23 | -0.66 | 1.72 | 1.65 | 1.86 | 0.21 | |||
苏氨酸Thr | 1.67 | 1.18 | 2.00 | 0.82 | AGG | 0.61 | 0.77 | 0.36 | -0.41 | ||
ACC | 0.75 | 0.71 | 0.78 | 0.07 | 甘氨酸Gly | 1.25 | 1.13 | 2.00 | 0.87 | ||
ACA | 1.10 | 1.25 | 1.22 | -0.03 | GGC | 0.45 | 0.35 | 0.45 | 0.10 | ||
ACG | 0.49 | 0.86 | 0.00 | -0.86 | GGA | 1.60 | 1.74 | 1.35 | -0.39 | ||
GGG | 0.70 | 0.78 | 0.20 | -0.58 |
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