桦木科叶绿体基因组密码子偏好性及系统发育分析

doi:10.13304/j.nykjdb.2022.0227

摘要/Abstract

摘要：

为分析桦木科叶绿体基因组编码区密码子的使用特征，利用CodonW1.4.2、Origin、SPSS25.0、 MEGA7.0软件和在线程序CUSP对50种桦木科植物叶绿体基因组密码子的偏好性及物种间的系统发育进行分析。结果表明，桦木科叶绿体基因组密码子适应指数（codon adaptation index，CAI）在0.163~0.166之间，平均0.165，有效密码子数（effective number of codon，ENC）范围在49.29~50.46之间，平均49.78，密码子偏好性弱。密码子不同位置的GC含量表现为GC1（45.4%）>GC2（37.4%）>GC3（29.7%），表明桦木科叶绿体密码子偏好于使用A/U结尾。ENC与密码子GC2、GC3及平均GC含量呈极显著正相关（P<0.01）。中性绘图、ENC-plot和PR2-plot分析表明，自然选择是桦木科叶绿体基因组密码子偏好性的主要影响因素。桦木科叶绿体基因组共有15个最优密码子，分别为CUC、CUG、AUC、GUC、GUG、GGG、UGC、CCA、ACG、GCC、CGA、CGG、CAG、GAG、AGG。基于同义密码子相对使用度（relative synonymous codon usage，RSCU）的聚类结果和基于matK基因序列构建的系统发育树在拓扑结构上具有相似性。以上研究结果为进一步对桦木科植物的资源利用、系统发育及叶绿体基因工程研究提供参考。

关键词: 桦木科, 叶绿体基因组, 密码子偏好性, 系统发育

Abstract:

To analyze the codon usage characteristics in the coding region of Betulaceae chloroplast genome， the chloroplast genome codon preferences and phylogenetic relationships among 50 Betulaceae species by CodonW1.4.2， Origin， SPSS25.0， MEGA7.0 and CUSP online program. The results showed that the codon adaptation index （CAI） of Betulaceae chloroplast genome ranged from 0.163 to 0.166， with an average value of 0.165， and the effective number of codon （ENC） ranged from 49.29 to 50.46， with an average value of 49.78， which indicated a weak codon preference among these species of Betulaceae. The GC content at different positions of codon showed GC1 （45.4%）>GC2 （37.4%）>GC3 （29.7%）， which indicated that chloroplast codons were prefer to A/U endings in Betulaceae. The correlation analysis showed that the ENC and GC2， GC3 and average GC showed an extremely significant level （P<0.01）. Analysis of neutral plot， ENC-plot and PR2-plot showed that natural selection was the main factor affecting the codon use preference of Betulaceae chloroplast genome. There were 15 optimal codons in the chloroplast genome of Betulaceae， which were CUC， CUG， AUC， GUC， GUG， GGG， UGC， CCA， ACG， GCC， CGA， CGG， CAG， GAG and AGG. The clustering results based on the relative synonymous codon usage （RSCU） were similar to the topological structure of phylogenetic tree based on matK gene sequence. The above results provided a reference for further research on resource utilization， phylogeny and chloroplast genetic engineering of Betulaceae.

Key words: Betulaceae, chloroplast genome, codon usage bias, phylogenetic

中图分类号:

S722

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.

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.

图/表 8

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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/%
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	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/%
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	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/%
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	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

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/%
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	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^**