Crops ›› 2025, Vol. 41 ›› Issue (6): 83-90.doi: 10.16035/j.issn.1001-7283.2025.06.011

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Chloroplast Genome Characteristics and Codon Bias Analysis of Anti-Broomrape Confectionery Sunflower Hybrid Jingkui 1408

Ma Jun1(), Zhang Xianglei2, An Chengjie2, Yang Xuewen3, Zhang Bolin2, Zhang Wu2(), Wang Pengdong4()   

  1. 1 Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
    2 College of Science, Jiamusi University, Jiamusi 154007, Heilongjiang, China
    3 College of Biology and Agriculture, Jiamusi University, Jiamusi 154007, Heilongjiang, China
    4 Research Institute of Economic Crops, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
  • Received:2024-07-26 Revised:2024-09-26 Online:2025-12-15 Published:2025-12-12

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Abstract:

In order to explore the chloroplast genome characteristics and codon bias of anti-broomrape confectionery sunflower hybrid Jingkui 1408, the whole genome data were obtained by high-throughput sequencing technology, and the chloroplast genome was assembled and annotated, and 50 coding sequences (CDS) were screened for codon bias analysis. The results showed that the total chloroplast genome of JK1408 was 151 100 bp, including a pair of inverted repeat regions, a large single-copy region, and a small single-copy region. A total of 129 genes were annotated, of which 85 genes encoded proteins, 8 genes encoded rRNA, and 36 genes encoded tRNA. The average GC content of GC1, GC2, GC3, and GCall in the 50 CDS sequences was 47.06%, 39.29%, 28.36% and 38.24%, respectively, and the average value of effective number of valid codons (ENC) was 47.62. Neutrality plot analysis and PR2-plot bias analysis showed that codon use bias was mainly influenced by natural selection; There are 20 244 codons in 50 CDS, and the optimal codons are CUU, CCA, ACU, GCU, UAU, CAU, AAA, GAU, and GGA.

Key words: Chloroplast genome, Codon bias, Sunflower

Fig.1

Physical map of the chloroplast genome in JK1408"

Table 1

Gene classification of the chloroplast genome in JK1408"

功能
Function		 家族
Family name		 基因代码
Code		 基因
Gene
复制基因
Duplicate gene		 核糖体小亚基
 rps
 rps11，rps12，rps12，rps14，rps15，rps16，rps18，rps19，rps2，rps3，rps4，rps7，rps7，rps8
rRNA rrn rrn16，rrn23，rrn4.5，rrn5，rrn5，rrn4.5，rrn23，rrn16
核糖体大亚基
 rpl
 rpl14，rpl16，rpl2，rpl2，rpl20，rpl22，rpl23，rpl23，rpl32，rpl33，rpl36
脱氧核糖核酸依赖性RNA聚合酶 rpo rpoA，rpoB，rpoC1，rpoC2
tRNA




 trn




 trnM-CAU，trnL-CAA，trnV-GAC，trnI-GAU，trnA-UGC，trnR-ACG，trnN-GUU，trnL-UAG，trnN-GUU，trnR-ACG，trnA-UGC，trnI-GAU，
trnV-GAC，trnL-CAA，trnM-CAU，trnP-UGG，trnW-CCA，trnM-CAU，trnV-UAC，trnF-GAA，trnL-UAA，trnT-UGU，trnS-GCU，trnfM-CAU，trnG-GCC，trnS-UGA，trnT-GGU，trnG-UCC，trnR-UCU，trnE-UUC，trnY-GUA，trnD-GUC，trnC-GCA，trnS-GCU，trnQ-UUG，trnH-GUG
光合作用基因
Photosynthesis gene
 ATP合酶亚基 atp atpA，atpB，atpE，atpF，atpH，atpI
NADH-脱氢酶亚基
 ndh
 ndhA，ndhB，ndhB，ndhC，ndhD，ndhE，ndhF，ndhG，ndhH，ndhI，ndhJ，ndhK
细胞色素b/f复合物的亚基 pet petA，petB，petD，petG，petL，petN
光系统I的亚基 psa psaA，psaB，psaC，psaI，psaJ，ycf3
光系统II的亚基
 psb
 psbH，psbA，psbB，psbC，psbD，psbE，psbF，psbL，psbI，psbJ，psbK，psbM，psbN，psbT，psbZ
二磷酸核酮糖氧合酶/羧化酶亚基 rbc rbcL
其他基因Other gene 乙酰辅酶A-羧化酶亚基 acc accD
包膜蛋白基因 cem cemA
c型细胞色素合成基因 ccs ccsA
蛋白酶基因 clp clpP
成熟酶基因 mat matK
平移起始因子 Inf infA
未知基因Unknown gene 假定叶绿体阅读框 ycf ycf1，ycf2，ycf2，ycf4

Table 2

GC contents and ENC values of codons at different locations in the chloroplast genome of JK1408"

基因
Gene		 GC1
(%)		 GC2
(%)		 GC3
(%)		 GCall
(%)		 有效密码子数
ENC		 基因
Gene		 GC1
(%)		 GC2
(%)		 GC3
(%)		 GCall
(%)		 有效密码子数
ENC
ycf4 44.32 40.54 30.27 38.38 51.04 psaA 52.86 43.68 32.76 43.10 49.59
ycf3 47.34 38.46 32.54 39.45 59.17 petD 51.55 39.13 27.33 39.34 39.25
ycf2 41.89 34.24 36.91 37.68 52.81 petB 49.07 41.67 27.31 39.35 43.52
ycf1 34.94 27.43 26.61 29.70 46.14 petA 52.65 37.38 30.84 40.29 50.97
rps8 41.48 40.74 28.15 36.79 48.57 ndhK 43.81 44.25 26.55 38.20 51.26
rps7 53.21 46.15 23.72 41.03 46.00 ndhJ 50.94 37.11 30.82 39.62 43.40
rps4 53.47 39.60 28.71 40.59 52.21 ndhI 41.92 35.93 25.75 34.53 43.82
rps3 46.12 33.33 23.74 34.40 43.16 ndhH 50.25 36.04 28.17 38.16 49.79
rps2 43.46 43.04 27.43 37.97 46.26 ndhG 45.76 33.90 28.25 35.97 52.00
rps18 34.31 42.16 25.49 33.99 44.76 ndhF 36.96 35.89 24.60 32.48 45.30
rps14 44.55 47.52 33.66 41.91 39.24 ndhE 42.16 34.31 18.63 31.70 43.98
rps11 54.74 55.47 27.01 45.74 50.38 ndhC 45.45 33.06 24.79 34.44 48.97
rpoC2 46.52 37.49 30.45 38.15 50.87 ndhB 41.29 38.55 32.09 37.31 48.60
rpoC1 50.29 36.52 26.23 37.68 48.88 ndhA 45.05 39.84 18.96 34.71 41.16
rpoB 50.52 37.32 27.80 38.55 48.50 matK 38.52 34.33 27.94 33.60 46.82
rpoA 44.35 32.14 29.76 35.42 51.62 clpP 59.39 38.07 30.46 42.64 50.07
rpl22 39.35 40.00 23.87 34.41 39.13 cemA 39.13 28.26 30.87 32.75 49.80
rpl20 37.80 45.67 27.56 37.01 46.96 ccsA 32.82 37.15 24.77 31.58 49.45
rpl2 50.18 47.27 33.45 43.64 56.40 atpI 50.40 37.90 28.23 38.84 46.54
rpl14 56.10 37.40 26.83 40.11 45.15 atpF 46.49 32.43 32.97 37.30 51.82
rbcL 57.00 43.00 30.86 43.62 47.42 atpE 52.96 41.04 25.37 39.80 51.30
psbD 52.26 43.22 32.49 42.66 44.10 atpB 55.71 41.68 29.06 42.15 48.21
psbC 53.38 46.20 29.54 43.04 43.82 atpA 56.19 39.49 25.15 40.27 46.83
psbB 53.83 45.97 30.45 43.42 47.88 accD 42.20 35.76 30.35 36.11 50.67
psbA 50.00 43.50 33.05 42.18 41.16 平均Average 47.06 39.29 28.36 38.24 47.62
psaB 48.03 43.40 29.25 40.23 46.17

Table 3

Correlation analysis between GC content and ENC value of codon number in chloroplast genome of JK1408"

指标
Index		 GC1 GC2 GC3 GCall 有效密码子数
ENC
GC2 0.389**
GC3 0.210 0.111
GCall 0.838** 0.737** 0.498**
有效密码子数ENC 0.084 -0.114 0.391** 0.121
密码子数N -0.141 -0.277* 0.280 -0.123 0.157

Table 4

RSCU analysis of amino acids in the chloroplast genome of JK1408"

氨基酸
Amino
acid		 密码子
Codon		 数目
Number		 相对
同义
密码子
RSCU		 氨基酸
Amino
acid		 密码子
Codon		 数目
Number		 相对
同义
密码子
RSCU
苯丙氨酸
Phe		 UUU 768 1.35 丙氨酸
Ala		 GCU 509 1.77
UUC 368 0.65 GCC 182 0.63
亮氨酸
Leu		 UUA 690 1.92 GCA 335 1.16
UUG 458 1.28 GCG 127 0.44
CUU 458 1.28 酪氨酸
Tyr		 UAU 628 1.63
CUC 128 0.36 UAC 142 0.37
CUA 289 0.81 组氨酸
His		 CAU 357 1.5
CUG 131 0.36 CAC 119 0.5
异亮氨酸
Ile		 AUU 836 1.46 谷氨酰胺
Gln		 CAA 570 1.53
AUC 340 0.6 CAG 176 0.47
AUA 536 0.94 天冬酰胺
Asn
 AAU 790 1.57
甲硫氨酸
Met		 AUG
 473
 1
 AAC
 214
 0.43
缬氨酸
Val		 GUU 395 1.46 赖氨酸
Lys		 AAA 788 1.49
GUC 133 0.49 AAG 267 0.51
GUA 410 1.51 天冬氨酸
Asp		 GAU 663 1.58
GUG 146 0.54 GAC 176 0.42
丝氨酸
Ser		 UCU 441 1.77 谷氨酸
Glu		 GAA 822 1.51
UCC 219 0.88 GAG 267 0.49
UCA 304 1.22 半胱氨酸
Cys		 UGU 157 1.45
UCG 119 0.48 UGC 60 0.55
AGU
 326
 1.31
 色氨酸
Trp		 UGG
 367
 1
AGC 82 0.33 精氨酸
Arg		 AGA 362 1.84
脯氨酸
Pro		 CCU 344 1.61 AGG 123 0.62
CCC 145 0.68 CGU 275 1.39
CCA 234 1.09 CGC 78 0.4
CCG 134 0.63 CGA 260 1.32
苏氨酸
Thr		 ACU 407 1.64 CGG 85 0.43
ACC 187 0.75 甘氨酸
Gly		 GGU 470 1.35
ACA 303 1.22 GGC 159 0.46
ACG 94 0.38 GGA 536 1.53
GGG 232 0.66

Fig.2

ENC-plot analysis in the chloroplast genome of JK1408"

Table 5

Frequency distribution of ENC ratio in the chloroplast genome of JK1408"

组段
Class range		 组中值
Class mid value		 频数
Frequency number		 频率
Frequency (%)
[-0.15,-0.05) -0.10 1 2
[-0.05,0.05) 0.00 22 44
[0.05,0.15) 0.10 20 40
[0.15,0.25) 0.20 6 12
[0.25,0.35) 0.30 1 2
合计Total 0.50 50 1

Fig.3

Neutrality plot analysis in the chloroplast genome of JK1408"

Fig.4

PR2-plot bias analysis in the chloroplast genome of JK1408"

Table 6

Determination of the optimal codon for the chloroplast genome of JK1408"

氨基酸
Amino
acid		 密码子
Codon		 高表达基因
High expression gene		 低表达基因
Low expression gene		 相对
使用度
差值
ΔRSCU		 氨基酸
Amino
acid		 密码子
Codon		 高表达基因
High expression gene		 低表达基因
Low expression gene		 相对
使用度
差值
ΔRSCU
数目
Number		 相对同义
密码子
RSCU		 数目
Number		 相对同义
密码子
RSCU		 数目
Number		 相对同义
密码子
RSCU		 数目
Number		 相对同义
密码子
RSCU
苯丙氨酸
Phe		 UUU 91 1.33 36 1.57 -0.24 丙氨酸
Ala		 GCU* 46 1.61 40 1.47 0.14
UUC* 86 0.67 24 0.43 0.24 GCC*** 22 0.90 7 0.28 0.62
亮氨酸
Leu		 UUA 67 1.74 51 2.33 -0.59 GCA 31 0.90 28 1.66 -0.76
UUG 77 1.24 25 1.39 -0.16 GCG 13 0.59 9 0.59 0.00
CUU* 82 1.31 28 1.08 0.23 酪氨酸
Tyr		 UAU* 91 1.45 28 1.34 0.11
CUC** 28 0.48 2 0.15 0.33 UAC 24 0.55 15 0.66 -0.11
CUA 48 0.84 27 0.90 -0.06 组氨酸
His		 CAU** 62 1.66 11 1.17 0.49
CUG* 26 0.39 5 0.14 0.24 CAC 17 0.34 7 0.43 -0.09
异亮氨酸
Ile		 AUU 99 1.29 55 1.77 -0.48 谷氨酰胺
Gln		 CAA 75 1.28 22 1.69 -0.41
AUC* 58 0.59 18 0.34 0.25 CAG** 38 0.72 4 0.31 0.41
AUA* 79 1.12 25 0.88 0.23 天冬酰胺
Asn
 AAU 130 1.40 34 1.44 -0.04
甲硫氨酸
Met		 AUG
 58
 1.00
 30
 1.00
 0.00
 AAC
 45
 0.60
 16
 0.56
 0.04
缬氨酸
Val		 GUU 36 0.98 27 1.85 -0.87 赖氨酸
Lys		 AAA* 120 1.62 34 1.39 0.23
GUC*** 23 0.64 4 0.14 0.50 AAG* 62 0.38 6 0.21 0.17
GUA 30 1.38 33 1.76 -0.38 天冬氨酸
Asp		 GAU* 123 1.61 24 1.36 0.25
GUG*** 27 0.10 4 0.25 0.74 GAC 30 0.39 6 0.64 -0.25
丝氨酸
Ser		 UCU 67 1.31 27 1.24 0.08 谷氨酸
Glu		 GAA 100 1.48 46 1.68 -0.19
UCC 47 1.05 16 1.31 -0.26 GAG* 54 0.52 11 0.32 0.19
UCA 57 1.41 19 1.65 -0.24 半胱氨酸
Cys		 UGU 21 1.32 8 1.80 -0.48
UCG** 30 0.71 3 0.27 0.44 UGC** 11 0.68 1 0.20 0.48
AGU*
 45
 1.34
 20
 1.20
 0.14
 色氨酸
Trp		 UGG
 47
 1.00
 26
 1.00
 0.00
AGC 14 0.17 6 0.32 -0.16 精氨酸
Arg		 CGU 32 2.17 20 2.42 -0.24
脯氨酸
Pro		 CCU 36 1.18 29 1.97 -0.79 CGC** 18 0.56 3 0.25 0.31
CCC* 26 0.84 9 0.57 0.27 CGA 38 1.02 12 1.15 -0.14
CCA* 41 1.26 15 1.07 0.19 CGG* 17 0.41 3 0.26 0.15
CCG** 18 0.72 6 0.39 0.33 AGA 61 1.25 15 1.59 -0.34
苏氨酸
Thr		 ACU* 48 1.59 22 1.40 0.19 AGG* 34 0.59 4 0.34 0.25
ACC* 22 0.77 11 0.64 0.12 甘氨酸
Gly		 GGU 45 1.05 48 1.77 -0.72
ACA 40 1.25 23 1.60 -0.35 GGC 9 0.19 10 0.32 -0.13
ACG 19 0.38 2 0.35 0.04 GGA*** 69 1.78 22 1.26 0.52
GGG** 40 0.97 8 0.64 0.33
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