甘蓝S-位点基因SRK、SLG和SP11/SCR密码子偏好性分析

doi:10.3724/SP.J.1006.2022.14003

Abstract

Abstract:

S-locus is the key locus in Brassica that controls the recognition and initiation of the self-incompatibility response. To clarify the codon usage characteristics of the S domain of S-locus genes SRK and SLG as well as of SP11/SCR coding sequence in Brassica oleracea, the codon usage bias of 41, 36, and 11 alleles of SRK, SLG, and SP11/SCR were analyzed by Codon W, SPSS, Python, and EMBOSS online tools, respectively. Neutrality, ENC-GC3, and Parity Rule 2 (PR2) plotting together with multivariate statistical analysis were also used for the exploration of possible factors that might affect the formation of the codon usage bias of these genes. The cluster analysis performed using various methods showed that S domains of SRK, SLG, and SP11/SCR genes of Brassica oleracea were rich in AT base pairs, the codon preference ended with A/T base and had a lower codon usage bias, which were affected by the natural selection (a main factor) and the mutational pressure (a secondary factor) as well as dinucleotide abundance. Based on the RSCU values, 4 over-expressed codons of SRK and SLG, and 11 over-expressed codons of SP11/SCR were identified. Cluster analysis based on RSCU could accurately reflect the relationship among SRK, SLG, and SP11/SCR alleles in Brassica oleracea, which was consistent and reliable with CDS sequence clustering. According to codon usage bias and cluster relationship, the S domain of SRK and the SP11/SCR coding sequence might be coevolutionary in the codon usage bias. This study enhances our understanding of the mechanism of distribution of codons and the evolution of SRK, SLG, and SP11/SCR genes in Brasscia oleracea.

Key words: Brassica oleracea, self-incompatibility, S-locus genes, codon usage bias, cluster analysis

ZHANG Yi-Zhong, ZENG Wen-Yi, DENG Lin-Qiong, ZHANG He-Cui, LIU Qian-Ying, ZUO Tong-Hong, XIE Qin-Qin, HU Deng-Ke, YUAN Chong-Mo, LIAN Xiao-Ping, ZHU Li-Quan. Codon usage bias analysis of S-locus genes SRK, SLG, and SP11/SCR in Brassica oleracea[J].Acta Agronomica Sinica, 2022, 48(5): 1152-1168.

Figures/Tables 14

Table 1

Information of SRK, SLG, and SP11/SCR alleles in Brassica oleracea"

序号 No.	基因登录号 Gene accession ID	基因名称 Gene name	类型 Class	参考文献 Reference	序号 No.	基因登录号 Gene accession ID	基因名称 Gene name	类型 Class	参考文献 Reference
1	AB054706.1	SRK1	I	Sato et al., 2002	45	X55275.1	SLG13	I	Dwyer et al., 1991
2	AB054709.1	SRK11	I	Sato et al., 2002	46	D85228.1	SLG14	I	Kusaba et al., 1997
3	AB180901.1	SRK12	I	Fujimoto et al., 2006	47	D85202.1	SLG16	I	Kusaba et al., 1997
4	AB024420.2	SRK13	I	Kusaba et al., 2000	48	AB054728.1	SLG20	I	Sato et al., 2002
5	AB298891.1	SRK14	I	Takuno et al., 2007	49	AB013719.1	SLG23	I	Kusaba et al., 1999
6	AB054710.1	SRK16	I	Sato et al., 2002	50	D85204.1	SLG25	I	Kusaba et al., 1997
7	AB054711.1	SRK20	I	Sato et al., 2002	51	D85205.1	SLG28	I	Kusaba et al., 1997
8	AB013720.1	SRK23	I	Kusaba et al., 1999	52	X16123.1	SLG29	I	Trick et al., 1989
9	AB054713.1	SRK25	I	Sato et al., 2002	53	X79431.1	SLG3	I	Delorme et al., 1995
10	AB190355.1	SRK28	I	Fujimot, 2004	54	D88765.1	SLG32	I	Kusaba et al., 1997
11	Z30211.1	SRK29	I	Kumar et al., 1994	55	AB054730.1	SLG33	I	Sato et al., 2002
12	X79432.1	SRK3	I	Delorme et al., 1995	56	D85206.1	SLG35	I	Kusaba et al., 1997
13	AB050482.1	SRK32	I	Kimura et al., 2000	57	AB054731.1	SLG36	I	Sato et al., 2002
14	AB054714.1	SRK33	I	Sato et al., 2002	58	D85207.1	SLG39	I	Kusaba et al., 1997
15	AB054715.1	SRK35	I	Sato et al., 2002	59	AB054732.1	SLG45	I	Sato et al., 2002
16	AB054716.1	SRK36	I	Sato et al., 2002	60	AB054733.1	SLG50	I	Sato et al., 2002
17	AB054718.1	SRK39	I	Sato et al., 2002	61	D85209.1	SLG51	I	Kusaba et al., 1997
18	AB054719.1	SRK45	I	Sato et al., 2002	62	D85210.1	SLG52	I	Kusaba et al., 1997
19	AB054720.1	SRK50	I	Sato et al., 2002	63	AB054734.1	SLG57	I	Sato et al., 2002
20	AB054721.1	SRK51	I	Sato et al., 2002	64	AB054735.1	SLG58	I	Sato et al., 2002
21	AB298901.1	SRK52	I	Takuno et al., 2007	65	Y00268.1	SLG6	I	Nasrallah et al., 1987
22	AB054722.1	SRK57	I	Sato et al., 2002	66	AB054736.1	SLG62	I	Sato et al., 2002
23	AB054723.1	SRK58	I	Sato et al., 2002	67	D85212.1	SLG64	I	Kusaba et al., 1997
24	M76647.1	SRK6	I	Stein et al., 1991	68	AB054737.1	SLG65	I	Sato et al., 2002
25	AB054724.1	SRK62	I	Sato et al., 2002	69	D85199.1	SLG7	I	Kusaba et al., 1997
26	AB054725.1	SRK64	I	Sato et al., 2002	70	AB054727.1	SLG8	I	Sato et al., 2002
27	AB054726.1	SRK65	I	Sato et al., 2002	71	D85211.1	SLG63	I	Kusaba et al., 1997
28	AB180898.1	SRK7	I	Fujimoto et al., 2006	72	D85208.1	SLG46	I	Kusaba et al., 1997
29	AB054708.1	SRK8	I	Sato et al., 2002	73	D85200.1	SLG9	I	Kusaba et al., 1997
30	AB054707.1	SRK7b	I	Sato et al., 2002	74	AB054729.1	SLG31	I	Sato et al., 2002
31	AB032473.1	SRK18	I	Suzuki et al., 2000	75	D85203.1	SLG17	I	Kusaba et al., 1997
32	AB298890.1	SRK4	I	Takuno et al., 2007	76	D85229.1	SLG22	I	Kusaba et al., 1997
33	AB298902.1	SRK61	I	Takuno et al., 2007	77	AB024415.1	SLG2	II	Kusaba et al., 2000
34	AB298905.1	SRK68	I	Takuno et al., 2007	78	AF195626.1	BoSCR13	I	Schopfer et al., 1999
35	AB054717.1	SRK38	I	Sato et al., 2002	79	EF577028.1	BoSCR13b	I	Lan et al., 2007
36	AB054712.1	SRK24	I	Sato et al., 2002	80	AJ278643.1	BoSCR3	I	Vanoosthuyse et al., 2001
37	AB024422.2	SRK13b	I	Kusaba et al., 2000	81	AB180900.1	BoSP11-12	I	Fujimoto et al., 2006
38	AB180903.1	SRK15	II	Fujimoto et al., 2006	82	AB176545.1	BoSP11-15	II	Shiba et al., 2004
39	AB024416.1	SRK2	II	Kusaba et al., 2000	83	AB067447.1	BoSP11-2	II	Shiba et al., 2002
40	Y18259.1	SRK5	II	Cabrillac et al., 1999	84	AB190356.1	BoSP11-28	I	Fujimoto, 2004
41	AB032474.1	SRK60	I	Suzuki et al., 2000	85	AB067448.1	BoSP11-5	II	Shiba et al., 2002
42	D85198.1	SLG1	I	Kusaba et al., 1997	86	AF195625	BoSCR6	I	Schopfer et al., 1999
43	AB326957.1	SLG11	I	Takuno et al., 2008	87	AB180898.1	BoSP11-7	I	Fujimoto et al., 2006
44	AB180902.1	SLG12	I	Fujimoto et al., 2006	88	AB180904.1	BoSP11A-15	II	Fujimoto et al., 2006

Table 1

Table 2

Table 3

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 4

Table 5

Table 6

Table 7

Fig. 5

Fig. 6

Fig. 7

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核苷酸组成和ENC Nucleotide composition and ENC	基因Gene
核苷酸组成和ENC Nucleotide composition and ENC	SRK	SLG	SP11/SCR
A (%)	27.47±0.50	27.30±0.45	29.68±1.42
T (%)	26.84±0.40	26.76±0.50	31.90±1.93
C (%)	20.56±0.42	20.72±0.47	16.49±1.87
G (%)	25.13±0.44	25.23±0.38	21.92±2.43
A3 (%)	20.11±0.93	20.07±0.96	27.79±3.76
T3 (%)	30.28±1.07	30.14±1.13	38.59±4.04
C3 (%)	24.46±1.12	24.54±0.95	16.47±3.46
G3 (%)	25.15±1.07	25.25±0.80	17.15±3.70
GC (%)	45.69±0.47	45.95±0.51	38.42±2.02
AT (%)	54.31±0.47	54.05±0.51	61.58±2.02
GC1 (%)	42.27±0.87	42.33±0.81	37.32±3.55
GC2 (%)	45.18±0.84	45.72±0.98	44.32±3.86
GC3 (%)	49.61±1.39	49.79±1.26	33.61±2.78
GC12 (%)	43.72±0.50	44.02±0.58	40.82±2.75
ENC	56.37±1.20	55.66±1.17	48.55±4.40

氨基酸 Amino acid	密码子 Codon	相对同义密码子RSCU			氨基酸 Amino acid	密码子 Codon	相对同义密码子RSCU
氨基酸 Amino acid	密码子 Codon	SRK	SLG	SP11/SCR	氨基酸 Amino acid	密码子 Codon	SRK	SLG	SP11/SCR
Phe	UUU	0.72	0.73	1.10	Thr	ACU	0.81	0.76	1.93
	UUC	1.28	1.27	0.90		ACC	0.97	1.04	0.33
Leu	UUA	0.25	0.21	2.38		ACA	1.44	1.46	1.52
	UUG	1.50	1.52	1.81		ACG	0.78	0.74	0.22
	CUU	1.93	2.06	0.16	Ala	GCU	1.67	1.78	2.45
	CUC	1.26	1.21	0.26		GCC	0.53	0.45	0.78
	CUA	0.39	0.37	0.89		GCA	1.06	1.04	0.57
	CUG	0.67	0.63	0.50		GCG	0.74	0.72	0.21
Ile	AUU	0.93	0.92	1.11	Gln	CAA	1.15	1.17	1.71
	AUC	1.24	1.31	0.71		CAG	0.85	0.83	0.29
	AUA	0.83	0.77	1.18	Asn	AAU	1.05	1.03	1.72
Val	GUU	0.69	0.64	2.22		AAC	0.95	0.97	0.28
	GUC	1.09	1.11	0.22	Lys	AAA	1.10	1.03	1.24
	GUA	0.56	0.54	0.57		AAG	0.90	0.97	0.76
	GUG	1.66	1.71	0.99	Asp	GAU	1.28	1.19	1.45
Ser	UCU	1.13	1.15	1.45		GAC	0.72	0.81	0.36
	UCC	0.66	0.68	0.30	Glu	GAA	0.68	0.70	1.53
	UCA	1.25	1.26	2.23		GAG	1.32	1.30	0.47
	UCG	0.67	0.61	0.64	Cys	UGU	1.52	1.51	1.16
	AGU	1.49	1.48	0.57		UGC	0.48	0.49	0.84
	AGC	0.81	0.81	0.81	Arg	CGU	0.31	0.29	1.17
Pro	CCU	0.99	1.08	2.30		CGC	0.20	0.19	1.08
	CCC	0.78	0.68	0.58		CGA	0.97	0.99	0.29
	CCA	1.33	1.33	0.51		CGG	0.87	0.92	0.35
	CCG	0.90	0.92	0.61		AGA	2.25	2.27	1.41
Tyr	UAU	0.71	0.71	1.59		AGG	1.41	1.34	1.70
	UAC	1.29	1.29	0.41	Gly	GGU	1.37	1.39	1.04
His	CAU	0.80	0.68	1.36		GGC	0.42	0.34	0.64
	CAC	1.15	1.32	0.45		GGA	1.01	1.02	2.03
						GGG	1.20	1.26	0.29

	A3%	T3%	C3%	G3%	GC3%	AT3%
A%	0.609^**	0.006	-0.321^*	-0.199	-0.410^**	0.410^**
T%	-0.070	0.534^**	-0.098	-0.370^*	-0.362^*	0.362^*
C%	-0.328^*	-0.157	0.447^**	-0.028	0.337^**	-0.337^*
G%	-0.314^*	-0.338^*	0.023	0.587^**	0.468^**	-0.468^**
GC%	1.000^**	-0.028	-0.422^**	-0.399^**	-0.645^**	0.645^**
AT%	0.581^**	0.459^**	-0.419^**	-0.524^**	-0.738^**	0.738^**

	A3%	T3%	C3%	G3%	GC3%	AT3%
A%	0.634^**	-0.343^*	-0.036	-0.232	-0.173	0.173
T%	-0.110	0.693^**	-0.500^**	-0.253	-0.537^**	0.537^**
C%	-0.206	-0.453^**	0.629^**	0.137	0.561^**	-0.561^**
G%	-0.347^*	0.057	-0.085	0.436^**	0.212	-0.212
GC%	-0.466^**	-0.366^*	0.523^**	0.452^**	0.681^**	-0.681^**
AT%	0.466^**	0.366^*	-0.523^**	-0.452^**	-0.681^**	0.681^**

	A3%	T3%	C3%	G3%	GC3%	AT3%
A%	0.257	-0.188	0.475	-0.500	-0.074	0.074
T%	-0.646^*	0.865^**	-0.374	0.061	-0.383	0.383
C%	0.719^*	-0.381	0.410	-0.700^*	-0.420	0.420
G%	-0.192	-0.286	-0.298	0.787^**	0.675^*	-0.675^*
GC%	0.436	-0.697^*	0.022	0.296	0.421	-0.421
AT%	-0.436	0.697^*	-0.022	-0.296	-0.421	0.421

Codon usage bias analysis of S-locus genes SRK, SLG, and SP11/SCR in Brassica oleracea

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基因 Gene	参数 Parameter	AA	AU	AG	AC	UU	UA	UC	UG
SRK	范围Range	0.76-0.91	0.88-1.06	0.87-1.03	0.98-1.20	0.71-0.85	0.62-0.73	1.03-1.34	1.07-1.23
	Mean±SD	0.84±0.03	0.97±0.05	0.94±0.04	1.01±0.05	0.80±0.04	0.67±0.03	1.23±0.06	1.17±0.04
	第一轴Axes1	0.039	-0.064	0.221	-0.115	0.294^*	-0.334^*	-0.227	0.274^*
SLG	范围Range	0.80-0.88	0.89-1.03	0.86-1.05	1.01-1.18	0.73-0.88	0.61-0.72	1.05-1.31	1.09-1.27
	Mean±SD	0.84±0.02	0.96±0.04	0.96±0.05	1.09±0.04	0.79±0.04	0.67±0.02	1.21±0.07	1.19±0.04
	第一轴Axes1	0.166	-0.044	-0.170	0.182	0.525^**	0.058	-0.537^**	0.108
SP11/SCR	范围Range	0.63-0.12	0.94-1.16	0.69-1.03	0.45-1.12	0.71-0.86	0.58-0.96	0.64-1.28	1.17-1.41
	Mean±SD	0.81±0.14	1.06±0.07	0.90±0.11	0.81±0.25	0.78±0.05	0.78±0.12	0.95±0.21	1.29±0.06
	第一轴Axes1	0.437	0.221	0.023	-0.383	0.110	-0.546^*	0.522^*	-0.224
基因 Gene	参数 Parameter	CC	CA	CU	CG	GG	GA	GU	GC
SRK	范围Range	0.65-0.92	0.96-1.17	0.95-1.23	0.71-1.00	0.75-0.91	1.16-1.35	0.85-1.05	0.59-0.81
	Mean±SD	0.82±0.06	1.09±0.05	1.10±0.06	0.83±0.06	0.85±0.03	1.25±0.05	0.94±0.04	0.71±0.05
	第一轴Axes1	0.283^*	0.226	-0.023	-0.342^*	-0.131	0.032	-0.145	0.236
SLG	范围Range	0.72-0.98	0.96-1.18	0.99-1.22	0.67-0.96	0.78-0.94	1.20-1.35	0.87-1.02	0.61-0.78
	Mean±SD	0.85±0.07	1.09±0.05	1.12±0.05	0.79±0.06	0.84±0.04	1.26±0.03	0.95±0.04	0.70±0.04
	第一轴Axes1	0.281^*	-0.002	-0.192	-0.159	0.087	-0.204	-0.407^**	0.291^*
SP11/SCR	范围Range	0.46-1.08	1.06-1.38	0.85-1.21	0.43-1.07	0.51-0.88	0.76-1.18	0.67-1.03	1.01-1.63
	Mean±SD	0.80±0.18	1.22±0.10	1.01±0.14	0.77±0.21	0.71±0.11	1.00±0.13	0.84±0.11	1.43±0.23
	第一轴Axes1	-0.054	0.260	-0.648^*	0.681^*	-0.451	-0.083	0.559^*	-0.172

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