Journal of Agricultural Science and Technology ›› 2023, Vol. 25 ›› Issue (10): 74-83.DOI: 10.13304/j.nykjdb.2022.0227
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Jiaxing GUO(), Xiang HUANG, Meihua YANG(
), Leilei WANG, Yanqi HAN, Zhuoyi LI
Received:
2022-03-24
Accepted:
2022-06-10
Online:
2023-10-15
Published:
2023-10-27
Contact:
Meihua YANG
郭佳星(), 黄祥, 杨梅花(
), 王蕾蕾, 韩彦奇, 李卓怡
通讯作者:
杨梅花
作者简介:
郭佳星 E-mail:gjxshz@sina.com;
基金资助:
CLC Number:
Jiaxing GUO, Xiang HUANG, Meihua YANG, Leilei WANG, Yanqi HAN, Zhuoyi LI. Analysis of Codon Usage Bias and Phylogenetic in Chloroplast Genome of Betulaceae[J]. Journal of Agricultural Science and Technology, 2023, 25(10): 74-83.
郭佳星, 黄祥, 杨梅花, 王蕾蕾, 韩彦奇, 李卓怡. 桦木科叶绿体基因组密码子偏好性及系统发育分析[J]. 中国农业科技导报, 2023, 25(10): 74-83.
编号 No. | 属 Genus | 种 Specie | 登录号 Accession No. | 密码子适应指数CAI | 有效密码子数ENC | GC含量GC content/% | |||
---|---|---|---|---|---|---|---|---|---|
GC1 | GC2 | GC3 | GC | ||||||
1 | 鹅耳枥属 Carpinus | 桦叶鹅耳枥 C. betulus | NC_039934.1 | 0.164 | 49.84 | 45.3 | 37.4 | 29.8 | 37.5 |
2 | 美洲鹅耳枥 C. caroliniana | NC_039935.1 | 0.164 | 49.84 | 45.3 | 37.3 | 29.8 | 37.5 | |
3 | 千金榆 C. cordata | KY312849.1 | 0.164 | 49.81 | 45.3 | 37.4 | 29.8 | 37.5 | |
4 | 川黔千金榆 C. fangiana | MG386371.1 | 0.164 | 49.78 | 45.3 | 37.3 | 29.8 | 37.5 | |
5 | 川陕鹅耳枥 C. fargesiana | NC_039937.1 | 0.164 | 49.86 | 45.3 | 37.4 | 29.8 | 37.6 | |
6 | 太鲁阁鹅耳枥 C. hebestroma | NC_038131.1 | 0.164 | 49.86 | 45.3 | 37.4 | 29.9 | 37.6 | |
7 | 云南鹅耳枥 C. monbeigiana | NC_039997.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.8 | 37.6 | |
8 | 宝华鹅耳枥 C. oblongifolia | NC_038092.1 | 0.164 | 49.87 | 45.3 | 37.4 | 29.9 | 37.6 | |
9 | 多脉鹅耳枥 C. polyneura | NC_039998.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.9 | 37.6 | |
10 | 紫脉鹅耳枥 C. purpurinervis | NC_038093.1 | 0.164 | 49.85 | 45.3 | 37.4 | 29.8 | 37.5 | |
11 | 普陀鹅耳枥 C. putoensis | KX695124.1 | 0.163 | 49.89 | 45.4 | 37.4 | 29.9 | 37.6 | |
12 | 岩生鹅耳枥 C. rupestris | NC_039999.1 | 0.164 | 49.87 | 45.3 | 37.4 | 29.8 | 37.6 | |
13 | 西藏鹅耳枥 C. tibetana | NC_052921.1 | 0.165 | 50.11 | 45.7 | 37.5 | 30.1 | 37.8 | |
14 | 天台鹅耳枥 C. tientaiensis | KY174338.1 | 0.166 | 50.46 | 47.1 | 38.8 | 31.0 | 39.0 | |
15 | 昌化鹅耳枥 C. tschonoskii | NC_039938.1 | 0.164 | 49.85 | 45.3 | 37.4 | 29.8 | 37.6 | |
16 | 雷公鹅耳枥 C. viminea | NC_039939.1 | 0.165 | 50.10 | 45.7 | 37.5 | 30.1 | 37.8 | |
17 | 虎榛子属 Ostryopsis | 虎榛子 O. davidiana | MG386376.1 | 0.165 | 49.79 | 45.2 | 37.2 | 29.8 | 37.4 |
18 | 中间虎榛子 O. intermedia | NC_040000.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.8 | 37.5 | |
19 | 滇虎榛 O. nobilis | NC_040001.1 | 0.164 | 49.89 | 45.3 | 37.4 | 29.8 | 37.5 | |
20 | 桦木属 Betula | 西桦 B. alnoides | MK888853.1 | 0.165 | 49.59 | 45.2 | 37.2 | 29.5 | 37.3 |
21 | 山纸皮桦 B. cordifolia | NC_037473.1 | 0.165 | 49.64 | 45.1 | 37.1 | 29.5 | 37.3 | |
22 | 硕桦 B. costata | MN830400.1 | 0.165 | 49.72 | 46.1 | 38.1 | 29.8 | 38.1 | |
23 | 盐桦 B. halophila | MG674393.1 | 0.165 | 49.29 | 45.5 | 37.3 | 28.9 | 37.3 | |
24 | 山桦 B. lenta | MG386366.1 | 0.165 | 49.65 | 45.2 | 37.3 | 29.5 | 37.4 | |
25 | 沼桦 B. nana | KX703002.1 | 0.165 | 49.68 | 45.1 | 37.1 | 29.6 | 37.3 | |
26 | 水桦 B. occidentalis | MG386367.1 | 0.165 | 49.64 | 45.2 | 37.3 | 29.5 | 37.4 |
Table 1 Parameters related to codon bias in chloroplast genome of Betulaceae
编号 No. | 属 Genus | 种 Specie | 登录号 Accession No. | 密码子适应指数CAI | 有效密码子数ENC | GC含量GC content/% | |||
---|---|---|---|---|---|---|---|---|---|
GC1 | GC2 | GC3 | GC | ||||||
1 | 鹅耳枥属 Carpinus | 桦叶鹅耳枥 C. betulus | NC_039934.1 | 0.164 | 49.84 | 45.3 | 37.4 | 29.8 | 37.5 |
2 | 美洲鹅耳枥 C. caroliniana | NC_039935.1 | 0.164 | 49.84 | 45.3 | 37.3 | 29.8 | 37.5 | |
3 | 千金榆 C. cordata | KY312849.1 | 0.164 | 49.81 | 45.3 | 37.4 | 29.8 | 37.5 | |
4 | 川黔千金榆 C. fangiana | MG386371.1 | 0.164 | 49.78 | 45.3 | 37.3 | 29.8 | 37.5 | |
5 | 川陕鹅耳枥 C. fargesiana | NC_039937.1 | 0.164 | 49.86 | 45.3 | 37.4 | 29.8 | 37.6 | |
6 | 太鲁阁鹅耳枥 C. hebestroma | NC_038131.1 | 0.164 | 49.86 | 45.3 | 37.4 | 29.9 | 37.6 | |
7 | 云南鹅耳枥 C. monbeigiana | NC_039997.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.8 | 37.6 | |
8 | 宝华鹅耳枥 C. oblongifolia | NC_038092.1 | 0.164 | 49.87 | 45.3 | 37.4 | 29.9 | 37.6 | |
9 | 多脉鹅耳枥 C. polyneura | NC_039998.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.9 | 37.6 | |
10 | 紫脉鹅耳枥 C. purpurinervis | NC_038093.1 | 0.164 | 49.85 | 45.3 | 37.4 | 29.8 | 37.5 | |
11 | 普陀鹅耳枥 C. putoensis | KX695124.1 | 0.163 | 49.89 | 45.4 | 37.4 | 29.9 | 37.6 | |
12 | 岩生鹅耳枥 C. rupestris | NC_039999.1 | 0.164 | 49.87 | 45.3 | 37.4 | 29.8 | 37.6 | |
13 | 西藏鹅耳枥 C. tibetana | NC_052921.1 | 0.165 | 50.11 | 45.7 | 37.5 | 30.1 | 37.8 | |
14 | 天台鹅耳枥 C. tientaiensis | KY174338.1 | 0.166 | 50.46 | 47.1 | 38.8 | 31.0 | 39.0 | |
15 | 昌化鹅耳枥 C. tschonoskii | NC_039938.1 | 0.164 | 49.85 | 45.3 | 37.4 | 29.8 | 37.6 | |
16 | 雷公鹅耳枥 C. viminea | NC_039939.1 | 0.165 | 50.10 | 45.7 | 37.5 | 30.1 | 37.8 | |
17 | 虎榛子属 Ostryopsis | 虎榛子 O. davidiana | MG386376.1 | 0.165 | 49.79 | 45.2 | 37.2 | 29.8 | 37.4 |
18 | 中间虎榛子 O. intermedia | NC_040000.1 | 0.164 | 49.88 | 45.3 | 37.4 | 29.8 | 37.5 | |
19 | 滇虎榛 O. nobilis | NC_040001.1 | 0.164 | 49.89 | 45.3 | 37.4 | 29.8 | 37.5 | |
20 | 桦木属 Betula | 西桦 B. alnoides | MK888853.1 | 0.165 | 49.59 | 45.2 | 37.2 | 29.5 | 37.3 |
21 | 山纸皮桦 B. cordifolia | NC_037473.1 | 0.165 | 49.64 | 45.1 | 37.1 | 29.5 | 37.3 | |
22 | 硕桦 B. costata | MN830400.1 | 0.165 | 49.72 | 46.1 | 38.1 | 29.8 | 38.1 | |
23 | 盐桦 B. halophila | MG674393.1 | 0.165 | 49.29 | 45.5 | 37.3 | 28.9 | 37.3 | |
24 | 山桦 B. lenta | MG386366.1 | 0.165 | 49.65 | 45.2 | 37.3 | 29.5 | 37.4 | |
25 | 沼桦 B. nana | KX703002.1 | 0.165 | 49.68 | 45.1 | 37.1 | 29.6 | 37.3 | |
26 | 水桦 B. occidentalis | MG386367.1 | 0.165 | 49.64 | 45.2 | 37.3 | 29.5 | 37.4 |
编号 No. | 属 Genus | 种 Specie | 登录号 Accession No. | 密码子适应指数CAI | 有效密码子数ENC | GC含量GC content/% | |||
---|---|---|---|---|---|---|---|---|---|
GC1 | GC2 | GC3 | GC | ||||||
27 | 桦木属 Betula | 白桦 B. platyphylla | MH205735.1 | 0.165 | 49.60 | 45.2 | 37.2 | 29.5 | 37.3 |
28 | 美国灰桦 B. populifolia | NC_039995.1 | 0.165 | 49.62 | 45.2 | 37.3 | 29.5 | 37.3 | |
29 | 欧洲桦 B. pubescens | MG386370.1 | 0.165 | 49.64 | 45.2 | 37.3 | 29.5 | 37.4 | |
30 | 桤木属 Alnus | 桤木 A. cremastogyne | NC_040996.1 | 0.165 | 49.66 | 45.4 | 37.4 | 29.5 | 37.5 |
31 | 欧洲桤木 A. glutinosa | NC_039930.1 | 0.165 | 49.87 | 45.3 | 37.4 | 29.8 | 37.6 | |
32 | 辽东桤木 A. incana | MG386364.1 | 0.165 | 49.83 | 45.2 | 37.3 | 29.8 | 37.5 | |
33 | 尼泊尔桤木 A. nepalensis | NC_039991.1 | 0.165 | 49.82 | 45.3 | 37.4 | 29.8 | 37.5 | |
34 | 红桤木 A. rubra | MG356709.1 | 0.165 | 49.75 | 45.2 | 37.3 | 29.7 | 37.4 | |
35 | 铁木属 Ostrya | 铁木 O. japonica | MG386375.1 | 0.164 | 49.77 | 45.2 | 37.2 | 29.8 | 37.5 |
36 | 天目铁木 O. rehderiana | KT454094.1 | 0.164 | 49.76 | 45.3 | 37.3 | 29.7 | 37.5 | |
37 | 毛果铁木 O. trichocarpa | KY088271.1 | 0.164 | 49.83 | 45.3 | 37.4 | 29.8 | 37.5 | |
38 | 榛属 Corylus | 美洲榛 C. americana | NC_045287.1 | 0.165 | 49.70 | 45.5 | 37.5 | 29.6 | 37.6 |
39 | 欧榛 C. avellana | KX822768.2 | 0.164 | 49.66 | 45.6 | 37.4 | 29.5 | 37.5 | |
40 | 华榛 C. chinensis | KX814336.2 | 0.164 | 49.65 | 45.5 | 37.4 | 29.5 | 37.5 | |
41 | 土耳其榛 C. colurna | NC_045290.1 | 0.165 | 49.74 | 45.5 | 37.4 | 29.6 | 37.6 | |
42 | 加州榛 C. cornuta | NC_045292.1 | 0.164 | 49.70 | 45.5 | 37.5 | 29.6 | 37.6 | |
43 | 披针叶榛 C. fargesii | MH628462.1 | 0.165 | 49.71 | 45.4 | 37.3 | 29.6 | 37.5 | |
44 | 刺榛 C. ferox | NC_045288.1 | 0.164 | 49.76 | 45.5 | 37.4 | 29.6 | 37.6 | |
45 | 榛 C. heterophylla | KX822769.2 | 0.164 | 49.67 | 45.6 | 37.4 | 29.6 | 37.6 | |
46 | 喜马拉雅榛 C. jacquemontii | NC_045291.1 | 0.164 | 49.72 | 45.5 | 37.5 | 29.6 | 37.6 | |
47 | 毛榛 C. mandshurica | MH628448.1 | 0.165 | 49.69 | 45.4 | 37.3 | 29.6 | 37.5 | |
48 | 日本榛 C. sieboldiana | NC_045289.1 | 0.165 | 49.71 | 45.5 | 37.4 | 29.6 | 37.6 | |
49 | 维西榛 C. wangii | NC_040995.1 | 0.165 | 49.73 | 45.4 | 37.3 | 29.6 | 37.5 | |
50 | 滇榛 C. yunnanensis | MH628461.1 | 0.165 | 49.71 | 45.4 | 37.3 | 29.6 | 37.5 | |
均值 Mean | 0.165 | 49.78 | 45.4 | 37.4 | 29.7 | 37.6 |
Table 1 Parameters related to codon bias in chloroplast genome of Betulaceae
编号 No. | 属 Genus | 种 Specie | 登录号 Accession No. | 密码子适应指数CAI | 有效密码子数ENC | GC含量GC content/% | |||
---|---|---|---|---|---|---|---|---|---|
GC1 | GC2 | GC3 | GC | ||||||
27 | 桦木属 Betula | 白桦 B. platyphylla | MH205735.1 | 0.165 | 49.60 | 45.2 | 37.2 | 29.5 | 37.3 |
28 | 美国灰桦 B. populifolia | NC_039995.1 | 0.165 | 49.62 | 45.2 | 37.3 | 29.5 | 37.3 | |
29 | 欧洲桦 B. pubescens | MG386370.1 | 0.165 | 49.64 | 45.2 | 37.3 | 29.5 | 37.4 | |
30 | 桤木属 Alnus | 桤木 A. cremastogyne | NC_040996.1 | 0.165 | 49.66 | 45.4 | 37.4 | 29.5 | 37.5 |
31 | 欧洲桤木 A. glutinosa | NC_039930.1 | 0.165 | 49.87 | 45.3 | 37.4 | 29.8 | 37.6 | |
32 | 辽东桤木 A. incana | MG386364.1 | 0.165 | 49.83 | 45.2 | 37.3 | 29.8 | 37.5 | |
33 | 尼泊尔桤木 A. nepalensis | NC_039991.1 | 0.165 | 49.82 | 45.3 | 37.4 | 29.8 | 37.5 | |
34 | 红桤木 A. rubra | MG356709.1 | 0.165 | 49.75 | 45.2 | 37.3 | 29.7 | 37.4 | |
35 | 铁木属 Ostrya | 铁木 O. japonica | MG386375.1 | 0.164 | 49.77 | 45.2 | 37.2 | 29.8 | 37.5 |
36 | 天目铁木 O. rehderiana | KT454094.1 | 0.164 | 49.76 | 45.3 | 37.3 | 29.7 | 37.5 | |
37 | 毛果铁木 O. trichocarpa | KY088271.1 | 0.164 | 49.83 | 45.3 | 37.4 | 29.8 | 37.5 | |
38 | 榛属 Corylus | 美洲榛 C. americana | NC_045287.1 | 0.165 | 49.70 | 45.5 | 37.5 | 29.6 | 37.6 |
39 | 欧榛 C. avellana | KX822768.2 | 0.164 | 49.66 | 45.6 | 37.4 | 29.5 | 37.5 | |
40 | 华榛 C. chinensis | KX814336.2 | 0.164 | 49.65 | 45.5 | 37.4 | 29.5 | 37.5 | |
41 | 土耳其榛 C. colurna | NC_045290.1 | 0.165 | 49.74 | 45.5 | 37.4 | 29.6 | 37.6 | |
42 | 加州榛 C. cornuta | NC_045292.1 | 0.164 | 49.70 | 45.5 | 37.5 | 29.6 | 37.6 | |
43 | 披针叶榛 C. fargesii | MH628462.1 | 0.165 | 49.71 | 45.4 | 37.3 | 29.6 | 37.5 | |
44 | 刺榛 C. ferox | NC_045288.1 | 0.164 | 49.76 | 45.5 | 37.4 | 29.6 | 37.6 | |
45 | 榛 C. heterophylla | KX822769.2 | 0.164 | 49.67 | 45.6 | 37.4 | 29.6 | 37.6 | |
46 | 喜马拉雅榛 C. jacquemontii | NC_045291.1 | 0.164 | 49.72 | 45.5 | 37.5 | 29.6 | 37.6 | |
47 | 毛榛 C. mandshurica | MH628448.1 | 0.165 | 49.69 | 45.4 | 37.3 | 29.6 | 37.5 | |
48 | 日本榛 C. sieboldiana | NC_045289.1 | 0.165 | 49.71 | 45.5 | 37.4 | 29.6 | 37.6 | |
49 | 维西榛 C. wangii | NC_040995.1 | 0.165 | 49.73 | 45.4 | 37.3 | 29.6 | 37.5 | |
50 | 滇榛 C. yunnanensis | MH628461.1 | 0.165 | 49.71 | 45.4 | 37.3 | 29.6 | 37.5 | |
均值 Mean | 0.165 | 49.78 | 45.4 | 37.4 | 29.7 | 37.6 |
指标 Index | 密码子适应指数CAI | 有效密码子数ENC | GC1 | GC2 | GC3 |
---|---|---|---|---|---|
有效密码子数ENC | -0.38* | ||||
GC1 | -0.03 | 0.14 | |||
GC2 | -0.24 | 0.50** | 0.72** | ||
GC3 | -0.33 | 0.94** | 0.10 | 0.45** | |
GC | -0.23 | 0.62** | 0.69** | 0.84** | 0.60** |
Table 2 Correlation analysis between the indexes of codon use
指标 Index | 密码子适应指数CAI | 有效密码子数ENC | GC1 | GC2 | GC3 |
---|---|---|---|---|---|
有效密码子数ENC | -0.38* | ||||
GC1 | -0.03 | 0.14 | |||
GC2 | -0.24 | 0.50** | 0.72** | ||
GC3 | -0.33 | 0.94** | 0.10 | 0.45** | |
GC | -0.23 | 0.62** | 0.69** | 0.84** | 0.60** |
1 | 匡可任.中国植物志:桦木科[M].北京:科学出版社,1979:44-150. |
KUANG K Z. Flora of China: Betulaceae [M]. Beijing: Science Press, 1979:44-150. | |
2 | 陈之端.桦木科植物的系统发育和地理分布[J].植物分类学报,1994,32(1):1-31. |
CHEN Z D. Phylogeny and phytogeography of the Betulaceae [J]. J. System. Evol., 1994, (1):1-31. | |
3 | 鲁志强.中国桦木科榛亚科的物种界定研究[D].兰州:兰州大学,2017. |
LU Z Q. Species delimitation in the subfamily Coryloideae of Betulaceae in China [D]. Lanzhou: Lanzhou University, 2017. | |
4 | 马会.转录组数据在桦木科生态适应、物种形成和系统发育研究中的应用初探[D].兰州:兰州大学,2014. |
MA H. An investigation on ecological adaptation, speciation and phylogeny in Betulaceae based on the transcriptome data [D]. Lanzhou: Lanzhou University, 2014. | |
5 | NIELSEN A Z, MELLOR S B, VAVITSAS K, et al.. Extending the biosynthetic repertoires of cyanobacteria and chloroplasts [J]. Plant J., 2016, 87(1):87-102. |
6 | TANG D, FAN W, KASHIF M H, et al.. Analysis of chloroplast differences in leaves of rice isonuclear alloplasmic lines [J]. Protoplasma, 2018, 255(1):1-9. |
7 | YAN M, ZHAO X, ZHOU J, et al.. The complete chloroplast genomes of Punica granatum and a comparison with other species in Lythraceae [J/OL]. Int. J. Mol. Sci., 2019, 20(12):2886 [2022-02-20]. . |
8 | 叶友菊,倪州献,白天道,等.马尾松叶绿体基因组密码子偏好性分析[J].基因组学与应用生物学,2018,37(10):4464-4471. |
YE Y J, NI Z X, BAI T D, et al.. The Analysis of chloroplast genome codon usage bais in Pinus massoniana [J]. Genom. Appl. Biol., 2018, 37 (10):4464-4471. | |
9 | SUEOKA N. Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses [J]. J. Mol. Evol., 2001, 53(4-5):469-476. |
10 | KOICHIRO T, JOEL D, MASATOSHI N, et al.. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. [J/OL]. Mol. Biol. Evol., 2007, (8):1596 [2022-02-20]. . |
11 | SHENG J J, SHE X, LIU X Y, et al.. Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species [J/OL]. Peer J., 2021, 23(9):12173 [2022-02-20]. . |
12 | 刘慧,王梦醒,岳文杰,等.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, et al.. Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.) [J]. Plant Sci. J., 2017, 35(3):362-371. | |
13 | PEDEN J F. Analysis of codon usage [D]. Nottingham: University of Nottingham, 1999. |
14 | ROMERO H, ZAVALA A, MUSTO H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces [J]. Nucleic Acids Res., 2000, 10:2084-2090. |
15 | XU C, CAI X, CHEN Q, et al.. Factors affecting synonymous codon usage bias in chloroplast genome of Oncidium Gower Ramsey [J]. Evol. Bio., 2011, 7:271-278. |
16 | ZHANG Y, NIE X, JIA X, et al.. Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family [J]. Aust. J. Bot., 2012, 60(5):461-470. |
17 | 杨霄月.桦木科叶绿体基因组的系统发育分析[D].兰州:兰州大学,2019. |
YANG X Y. Phylogenetic analysis of Betulaceae plastomes [D]. Lanzhou: Lanzhou University, 2019. | |
18 | 于涛,张宇阳,高健,等.极小种群濒危植物盐桦叶绿体基因组特征分析[J].林业科学,2019,55(2):41-49. |
YU T, ZHANG Y Y, GAO J, et al.. Complete chloroplast genome sequence of Betula halophila,a plant species with extremely small populations [J]. Sci. Silvae Sin., 2019, 55 (2):41-49. | |
19 | LEE S I, NKONGOLO K, PARK D, et al.. Characterization of chloroplast genomes of Alnus rubra and Betula cordifolia, and their use in phylogenetic analyses in Betulaceae [J]. Genes Genom., 2019, 41(3):305-316. |
20 | 丁锐,胡兵,宗小雁,等.杓兰叶绿体基因组密码子偏好性分析[J].林业科学研究,2021,34(5):177-185. |
DING R, HU B, ZONG X Y, et al.. Analysis of codon usage in the chloroplast genome of Cypripedium calceolus [J]. For. Res., 2021, 34 (5):177-185. | |
21 | 尚明照,刘方,华金平,等.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, et al.. Analysis on codon usage of chloroplast genome of Gossypium hirsutum [J]. Sci. Agric. Sin., 2011, 44 (2):245-253. | |
22 | RUTH H, DMITRI A. Selection on Codon Bias [J]. Annu. Rev. Genet., 2008, 42:287-299. |
23 | 李凤,辛静,辛雅萱,等.楸树叶绿体基因组密码子偏性分析[J].南方农业学报,2021,52(10):2735-2743. |
LI F, XIN J, XIN Y X, et al.. Codon usage bias of chloroplast genome in Catalpa bungei C. A. Mey. [J]. J. Southern Agric, 2021, 52(10):2735-2743. | |
24 | MURRAY E E, LOTZER J, EBERLE M. Codon usage in plant genes [J]. Nucl. Acids Res., 1989, 17(2):477-498. |
25 | 赵森,邓力华,陈芬.秋茄叶绿体基因组密码子使用偏好性分析[J].森林与环境学报,2020,40(5):534-541. |
ZHAO S, DENG L H, CHEN F. Codon usage bias of chloroplast genome in Kandelia obovata [J]. J. For. Environ., 2020, 40(5):534-541. | |
26 | SHARP P M, STENICO M, PEDEN J F. Codon usage: mutational bias, translation selection, or both? [J]. Biochem. Soc. T., 1993, 4:835-841. |
27 | KAWABE A, MIYASHITA N T. Patterns of codon usage bias in three dicot and four monocot plant species [J]. Genes Genet. Syst., 2003, 5:343-352. |
28 | 季凯凯,宋希强,陈春国,等.木兰科叶绿体基因组的密码子使用特征分析[J].中国农业科技导报,2020,22(11):52-62. |
JI K K, SONG X Q, CHEN C G, et al.. Codon usage profiling of chloroplast genome in Magnoliaceae [J]. J. Agric. Sci.Technol., 2020, 22(11):52-62. | |
29 | 沈宗芳,陆添权,张志荣,等.槲蕨属叶绿体基因组密码子偏好性分析[J].广西植物, 2021,41(2):266-273. |
SHEN Z F, LU T Q, ZHANG Z R, et al.. Condon preference of chloroplast genome of Drynaria [J]. Guihaia, 2021, 41(2):266-273. | |
30 | 王占军,李豹,姜行舟,等.两种茶树全基因组数据的密码子偏好性比较分析[J].中国细胞生物学学报,2018,40(12):62-73. |
WANG Z J, LI B, JIANG X Z, et al.. Comparative analysis of the codon preference patterns in two species of Camellia sinensis based on genome data [J]. Chin. J. Cell Biol., 2018, 40(12):62-73. | |
31 | 周猛,童春发,施季森.杨树同义密码子用法的初步分析[J].植物生理与分子生物学学报,2007,33(4):285-293. |
ZHOU M, TONG C F, SHI J S. A preliminary analysis of synonymous codon usage in poplar species [J]. J. Plant Physiol. Mol. Biol.,2007, 33(4):285-293. | |
32 | 原晓龙,李云琴,王毅,等.西南桦叶绿体基因组密码子偏好性分析[J].基因组学与应用生物学,2020,39(12):5758-5764. |
YUAN X L, Li Y Q, WANG Y, et al.. Analysis of codon usage in the chloroplast genome of Betula alnoides [J]. Genome Appl. Biol., 2020, 39 (12):5758-5764. | |
33 | 赖瑞联,林玉玲,钟春水,等.龙眼生长素受体基因TIR1密码子偏好性分析[J].园艺学报.2016,43(4):771-780. |
LAI R L, LIN Y L, ZHONG C S, et al.. Analysis of codon bias of auxin receptor gene TIR1 in Dimocarpus longan [J]. Acta Hortic. Sin., 2016, 43(4):771-780. |
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