马尾松转录组密码子使用偏好性及其影响因素

doi:10.11707/j.1001-7488.20200408

摘要/Abstract

摘要：

目的: 异源表达是植物蛋白功能验证和分子育种的重要手段，而密码子是异源基因高效表达的重要因素，对马尾松转录组基因编码区密码子偏好性分析可以为马尾松分子育种提供一定的理论支持。方法: 利用CodonW、EMBOSS密码子分析软件对马尾松转录组进行密码子参数分析和密码子偏好性分析，根据中性绘图、ENc-GC3s、偏倚性分析推测马尾松密码子偏好性的主要形成原因。通过比较高低表达基因样本同义密码子相对使用度（RSCU）筛选马尾松最优密码子，通过密码子使用频率比值分析马尾松与拟南芥、烟草、欧洲山杨、大肠杆菌、酿酒酵母的密码子偏好性差异。结果: 马尾松转录组编码序列（CDS）密码子平均GC含量为44.95%，密码子第3位GC含量为38.95%，尤为偏好A/T。高、低表达基因样本统计分析表明，马尾松转录组RSCU差异较小，筛选出TTA、CAA、TGT、GGT等27个密码子可作为马尾松的最优密码子。中性绘图、ENc-GC3s关联分析以及偏倚分析表明，马尾松密码子偏好性的形成可能主要受突变影响，其次受自然选择等多重因素共同影响。密码子使用频率分析表明马尾松密码子偏好性与烟草、拟南芥和欧洲山杨相比差异较小，与大肠杆菌差异最大，与酿酒酵母差异小于大肠杆菌。结论: 马尾松偏好第3位为A/T的密码子，筛选出27个最优密码子，其中25个密码子第3位为A/T。马尾松密码子使用偏好性形成主要受突变影响，其次受自然选择等多重因素共同影响。烟草可以作为马尾松基因异源表达的优选植物生物体，而微生物中酿酒酵母可能优于大肠杆菌。

关键词: 马尾松, 转录组, 密码子使用偏好性

Abstract:

Objective: Heterologous expression is an important means of plant protein function verification and molecular breeding. Codons are important factors for efficient expression of heterologous genes. An analysis of codon bias of gene coding region of Pinus massoniana transcriptome was conducted in order to provide a theoretical basis for molecular breeding of P. massoniana. Method: Analysis of codon parameters and bias in P. massoniana transcriptome by using CodonW, EMBOSS and other codon analysis software. According to the neutral mapping, ENc-GC3s correlation analysis and bias analysis speculates the main reasons for codon bias. The optimal codons of P. massoniana were screened by comparing the relative synonymous codon usage(RSCU) of high and low expression gene samples, and the codon bias differences between P. massoniana and Arabidopsis thaliana, Nicotiana tabacum, Populus tremula, Escherichia coli and Saccharomyces cerevisiae were analyzed by codon usage frequency ratio. Result: The average GC content of P. massoniana transcriptome coding sequence(CDS) codon was 44.95%, and GC content in the third position of codon was 38.95%, especially preferred A/T. Statistical analysis of high and low expression gene samples indicated that the difference of the relative synonymous codon usage (RSCU) in the transcriptome of P. massoniana was small, the 27 codons such as TTA, CAA, TGT and GGT can be used as the optimal codons for P. massoniana. Neutral mapping, ENc-GC3s correlation analysis and bias analysis showed that the formation of P. massoniana codon preference may be mainly affected by mutation, and secondly affected by multiple factors such as natural selection. Codon usage frequency analysis showed that the codon bias in P. massoniana was less different from N. tabacum, A. thaliana and P. tremula. The difference with E. coli was the largest, and the difference with S. cerevisiae was smaller than E. coli. Conclusion: Among the 27 optimal codons screened, 25 codons have the third one as A/T. P. massoniana prefers the third codon as A/T. The formation of P. massoniana codon preference may be mainly affected by mutation, and secondly affected by multiple factors such as natural selection. N. tabacum is the preferred plant organisms for heterologous expression of P. massoniana and S. cerevisiae may be superior to E. coli in the microorganism.

Key words: Pinus massoniana, transcriptome, codon usage bias

中图分类号:

S718.46

朱沛煌,陈妤,朱灵芝,李荣,季孔庶. 马尾松转录组密码子使用偏好性及其影响因素[J]. 林业科学, 2020, 56(4): 74-81.

Peihuang Zhu,Yu Chen,Lingzhi Zhu,Rong Li,Kongshu Ji. Codon Usage Bias and Its Influencing Factors in Pinus massoniana Transcriptome[J]. Scientia Silvae Sinicae, 2020, 56(4): 74-81.

图/表 5

图1

图2

图3

表1

马尾松转录组最优密码子分析①"

氨基酸 Amino acid	密码子 Codon	低表达基因 Low expressed genes		高表达基因 High expressed genes		ΔRSCU
氨基酸 Amino acid	密码子 Codon	RSCU	出现次数 Number	RSCU	出现次数 Number	ΔRSCU
Phe	TTT^*	1.09	1 452	1.32	1 381	0.23
	TTC	0.91	1 180	0.68	830	-0.23
Leu	TTA^*	0.77	711	1.05	917	0.28
	TTG^*	1.38	1 245	1.67	1 363	0.29
	CTT^*	1.21	1 120	1.42	1 136	0.21
	CTC	0.92	890	0.51	440	-0.41
	CTA	0.56	544	0.56	358	0
	CTG	1.17	1 084	0.79	614	-0.38
Ile	ATT^*	1.35	1 410	1.60	1 704	0.25
	ATC	0.82	878	0.59	703	-0.23
	ATA	0.83	872	0.80	700	-0.03
Met	ATG	1.00	1 737	1.00	1 569	0
Val	GTT^*	1.36	1 369	1.69	1 615	0.33
	GTC	0.74	819	0.53	467	-0.21
	GTA^*	0.72	730	0.82	716	0.10
	GTG	1.18	1 220	0.96	895	-0.22
Tyr	TAT^*	1.16	950	1.43	1 165	0.27
	TAC	0.84	740	0.57	529	-0.27
TER	TAA	1.04	105	1.20	133	0.16
	TAG	0.66	58	0.59	53	-0.07
His	CAT^*	1.18	804	1.49	1 000	0.31
	CAC	0.82	600	0.51	361	-0.31
Gln	CAA^*	0.91	1 129	1.14	1 446	0.23
	CAG	1.09	1 370	0.86	880	-0.23
Asn	AAT^*	1.22	1 616	1.43	1 751	0.21
	AAC	0.78	1 061	0.57	789	-0.21
Lys	AAA^*	0.94	1 887	1.07	2 250	0.13
	AAG	1.06	2 155	0.93	1 755	-0.13
Asp	GAT^*	1.27	2 031	1.49	2 041	0.22
	GAC	0.73	1 131	0.51	739	-0.22
Glu	GAA^*	1.06	2 196	1.22	2 264	0.16
	GAG	0.94	1 943	0.78	1 346	-0.16
Ser	TCT^*	1.33	1 185	1.78	1 300	0.45
	TCC	0.96	909	0.59	478	-0.37
	TCA^*	1.11	973	1.67	1 217	0.56
	TCG	0.73	683	0.25	211	-0.48
Pro	CCT^*	1.35	1 013	1.65	1 148	0.30
	CCC	0.88	669	0.47	372	-0.41
	CCA^*	1.14	866	1.65	1 198	0.51
	CCG	0.62	508	0.23	172	-0.39
Thr	ACT^*	1.20	878	1.53	1 088	0.33
	ACC	0.87	698	0.57	467	-0.30
	ACA^*	1.30	911	1.65	1 163	0.35
	ACG	0.63	474	0.25	175	-0.38
Ala	GCT^*	1.24	1 420	1.64	1 893	0.40
	GCC	0.92	1 123	0.53	670	-0.39
	GCA^*	1.27	1 450	1.62	1 489	0.35
	GCG	0.57	692	0.21	260	-0.36
Cys	TGT^*	0.97	605	1.27	621	0.30
	TGC	1.03	665	0.73	310	-0.30
TER	TGA	1.30	117	1.21	94	-0.09
Trp	TGG	1.00	781	1.00	680	0
Arg	CGT^*	0.76	466	0.86	566	0.10
	CGC	0.76	497	0.33	154	-0.43
	CGA	0.80	462	0.67	406	-0.13
	CGG	0.73	466	0.41	160	-0.32
Ser	AGT^*	0.90	821	1.08	804	0.18
	AGC	0.98	875	0.62	448	-0.36
Arg	AGA^*	1.53	914	2.15	1 157	0.62
	AGG^*	1.41	866	1.58	668	0.17
Gly	GGT^*	0.99	1 043	1.32	1 606	0.33
	GGC	0.89	976	0.61	615	-0.28
	GGA^*	1.23	1 262	1.38	1 451	0.15
	GGG	0.89	939	0.68	577	-0.21

表1

图4

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