Genome-wide Analysis of Codon Usage Bias in Saccharum Species and Its Phylogenetically Related Species Erianthus fulvus

doi:10.13560/j.cnki.biotech.bull.1985.2023-0982

Abstract

Abstract:

【Objective】 To clarify the codon usage characteristics and improve expression efficiency of exogenous genes in sugarcane. 【Method】 Codon usage bias were analyzed by Python and CodonW1.4.2 tools based on their genomes data of three species including Saccharum officinarum (LA-purple), S. sponaneum (NP-X and AP85-441), and Erianthus fulvus (Yunnan2009-3). Neutrality-plot, ENC-plot, and Parity Rule 2（PR2）-plot analysis were also used to explore the possible factors that affect the formation of codon usage bias. Simultaneously, correlation analysis between gene expressions and codon usage bias parameters was carryd out based on transcriptome data. Finally, a comparison analysis of codon usage patterns were performed between sugarcane and the other seven main model organisms, namely, Zea mays, Sorghum bicolor, Oryza sativa, Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli, and Saccharomyces cerevisiae based on the average RSCU value of three species. 【Result】 S. officinarum, S. sponaneum, and E. fulvus were rich in GC base pairs, the average GC content was 56.3%, and GC3 was the highest, followed by GC1 and GC2, indicating that sugarcane preferred to use synonymous codons ending with a C/G base. The average ENC value was 48.45, suggesting that sugarcane had a lower codon usage bias. According to the results of neutral-plot, ENC-plot, and PR2-plot analysis, the codon usage bias of four genomes was affected by natural selection, mutation pressure, and so on, and the natural selection dominated in them. Correlation analysis showed that codon preference parameters were significantly correlated with the actual transcription expressions of genes, but the correlation was not strong. Based on the RSCU and ∆RSCU values, thirteen identical optimal codons were confirmed, and all of them were ended with C/G base pairs. The codon usage characteristics were not different at genome-wide and chromosome level. In addition, the codon usage bias of sugarcane was similar to that of Z. mays, S. bicolor, and O. sativa, while it had a significant difference with A. thaliana, N. tabacum, E. coli, and S. cerevisiae. 【Conclusion】 The codon usage bias among S. officinarum, S.sponaneum and E. fulvus was highly similar, and its formation was affected by natural selection and mutation pressure factors. Meanwhile, Z. mays, O. sativa and S. bicolor could be used for elite gene function research on sugarcane as a exogenous expression system on account of their codon usage bias patterns.

Key words: Saccharum, Erianthus fulvus, genome, codon usage bias, optimal codons

TIAN Chun-yan, LI Xu-juan, LI Chun-jia, MAO Jun, LIU Xin-long. Genome-wide Analysis of Codon Usage Bias in Saccharum Species and Its Phylogenetically Related Species Erianthus fulvus[J]. Biotechnology Bulletin, 2024, 40(3): 202-214.

Figures/Tables 10

References 40

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核苷酸组成和ENC Nucleotide composition and ENC	材料 Materials				平均值 Mean
核苷酸组成和ENC Nucleotide composition and ENC	LA-purple	NP-X	AP85-441	Yunnan2009-3	平均值 Mean
A3s/%	15.61±8.47	15.65±8.14	14.91±8.01	16.41±8.38	15.65
T3s/%	20.19±11.13	19.95±10.52	19.00±10.41	21.14±10.95	20.07
G3s/%	31.24±8.23	31.11±7.78	31.95±7.95	30.42±7.84	31.18
C3s/%	32.97±12.91	33.28±12.31	34.14±12.13	32.04±12.66	33.11
GC/%	56.21±0.10	56.42±0.09	57.53±0.09	55.02±0.09	56.30
GC1/%	58.39±7.29	58.53±6.76	59.29±6.80	57.67±6.86	58.47
GC2/%	45.73±7.79	46.05±7.34	46.87±7.57	44.67±7.06	45.83
GC3/%	64.21±18.91	64.39±18.02	66.09±17.78	62.46±18.68	64.29
GC3s/%	62.89±0.20	63.10±0.19	64.91±0.18	61.06±0.19	62.99
ENC	47.97±9.11	48.74±8.93	48.19±9.26	48.89±8.82	48.45

核苷酸组成和ENC Nucleotide composition and ENC	材料 Materials				平均值 Mean
核苷酸组成和ENC Nucleotide composition and ENC	LA-purple	NP-X	AP85-441	Yunnan2009-3	平均值 Mean
A3s/%	15.61±8.47	15.65±8.14	14.91±8.01	16.41±8.38	15.65
T3s/%	20.19±11.13	19.95±10.52	19.00±10.41	21.14±10.95	20.07
G3s/%	31.24±8.23	31.11±7.78	31.95±7.95	30.42±7.84	31.18
C3s/%	32.97±12.91	33.28±12.31	34.14±12.13	32.04±12.66	33.11
GC/%	56.21±0.10	56.42±0.09	57.53±0.09	55.02±0.09	56.30
GC1/%	58.39±7.29	58.53±6.76	59.29±6.80	57.67±6.86	58.47
GC2/%	45.73±7.79	46.05±7.34	46.87±7.57	44.67±7.06	45.83
GC3/%	64.21±18.91	64.39±18.02	66.09±17.78	62.46±18.68	64.29
GC3s/%	62.89±0.20	63.10±0.19	64.91±0.18	61.06±0.19	62.99
ENC	47.97±9.11	48.74±8.93	48.19±9.26	48.89±8.82	48.45

ENC值 ENC value	LA-purple		NP-X		AP85-441		Yunnan2009-3
ENC值 ENC value	数目	百分比/%	数目	百分比/%	数目	百分比/%	数目	百分比/%
ENC≤35	34 381	14.15	15 880	12.10	8 642	14.23	4 290	12.05
35<ENC≤45	46 920	19.32	24 450	18.64	11 548	19.07	5 955	16.72
ENC˃45	161 603	66.53	90 849	69.26	40 414	66.70	25 371	71.23

ENC值 ENC value	LA-purple		NP-X		AP85-441		Yunnan2009-3
ENC值 ENC value	数目	百分比/%	数目	百分比/%	数目	百分比/%	数目	百分比/%
ENC≤35	34 381	14.15	15 880	12.10	8 642	14.23	4 290	12.05
35<ENC≤45	46 920	19.32	24 450	18.64	11 548	19.07	5 955	16.72
ENC˃45	161 603	66.53	90 849	69.26	40 414	66.70	25 371	71.23

氨基酸 Amino acid	密码子 Codon	LA-purple				NP-X				AP85-441				Yunnan2009-3
氨基酸 Amino acid	密码子 Codon	GW	HEB	LEB	∆RSCU	GW	HEB	LEB	∆RSCU	GW	HEB	LEB	∆RSCU	GW	HEB	LEB	∆RSCU
Phe	UUU	0.76	0.05	0.95	-0.90	0.73	0.06	0.95	-0.89	0.69	0.19	0.93	-0.74	0.78	0.06	0.96	-0.90
	UUC**	1.24	1.95	1.05	0.90	1.27	1.94	1.05	0.89	1.31	1.81	1.07	0.74	1.22	1.94	1.04	0.90
Leu	UUA	0.39	0.01	0.53	-0.52	0.37	0.01	0.52	-0.51	0.33	0.04	0.51	-0.47	0.41	0.01	0.53	-0.52
	UUG	0.94	0.14	1.11	-0.97	0.92	0.16	1.11	-0.95	0.86	0.08	1.10	-1.02	0.97	0.15	1.12	-0.97
	CUU	1.04	0.13	1.27	-1.14	1.03	0.15	1.24	-1.09	1.00	1.30	1.26	0.04	1.08	0.14	1.26	-1.12
	CUC**	1.59	2.99	1.20	1.79	1.60	2.95	1.21	1.74	1.72	2.09	1.23	0.86	1.51	2.94	1.19	1.75
	CUA	0.50	0.07	0.66	-0.59	0.50	0.08	0.67	-0.59	0.46	0.88	0.65	0.23	0.54	0.08	0.67	-0.59
	CUG**	1.54	2.65	1.24	1.41	1.58	2.65	1.24	1.41	1.64	1.61	1.26	0.35	1.49	2.67	1.22	1.45
Ile	AUU	1.04	0.10	1.17	-1.07	1.01	0.11	1.16	-1.05	0.97	0.31	1.17	-0.86	1.05	0.12	1.17	-1.05
	AUC**	1.34	2.81	1.04	1.77	1.35	2.78	1.04	1.74	1.43	2.48	1.05	1.43	1.29	2.78	1.03	1.75
	AUA	0.63	0.09	0.78	-0.69	0.64	0.10	0.79	-0.69	0.60	0.21	0.78	-0.57	0.66	0.10	0.80	-0.70
Val	GUU	0.95	0.09	1.23	-1.14	0.94	0.1	1.21	-1.11	0.90	0.78	1.22	-0.44	1.00	0.09	1.23	-1.14
	GUC	1.15	1.69	0.97	0.72	1.17	1.69	0.99	0.70	1.22	1.48	0.99	0.49	1.12	1.67	0.97	0.70
	GUA	0.41	0.04	0.58	-0.54	0.41	0.05	0.58	-0.53	0.38	0.53	0.57	-0.04	0.44	0.05	0.59	-0.54
	GUG**	1.48	2.18	1.22	0.96	1.48	2.17	1.22	0.95	1.50	1.21	1.01	0.20	1.44	2.19	1.21	0.98
Ser	UCU	1.03	0.15	1.17	-1.02	1.00	0.16	1.16	-1.00	0.96	0.58	1.14	-0.56	1.06	0.16	1.17	-1.01
	UCC**	1.25	2.24	1.06	1.18	1.24	2.18	1.07	1.11	1.32	1.85	1.08	0.77	1.19	2.17	1.03	1.14
	UCA	0.99	0.13	1.18	-1.05	0.99	0.14	1.17	-1.03	0.94	0.33	1.16	-0.83	1.04	0.14	1.20	-1.06
	UCG	0.80	1.65	0.68	0.97	0.81	1.64	0.69	0.95	0.87	1.21	0.70	0.51	0.76	1.66	0.68	0.98
	AGU	0.72	0.07	0.85	-0.78	0.70	0.08	0.85	-0.77	0.64	0.30	0.84	-0.54	0.75	0.08	0.87	-0.79
	AGC**	1.22	1.76	1.05	0.71	1.25	1.80	1.07	0.73	1.27	1.73	1.07	0.66	1.20	1.79	1.05	0.74
Pro	CCU	0.98	0.20	1.15	-0.95	0.96	0.21	1.13	-0.92	0.92	1.20	1.14	0.06	1.02	0.21	1.17	-0.96
	CCC	0.88	1.38	0.80	0.58	0.88	1.36	0.81	0.55	0.92	0.95	0.82	0.13	0.85	1.36	0.79	0.57
	CCA	1.03	0.20	1.20	-1.00	1.03	0.22	1.20	-0.98	0.96	0.70	1.18	-0.48	1.08	0.21	1.22	-1.01
	CCG	1.11	2.22	0.85	1.37	1.12	2.21	0.85	1.36	1.20	1.14	0.86	0.28	1.05	2.22	0.82	1.40
Thr	ACU	0.95	0.10	1.13	-1.03	0.91	0.11	1.12	-1.01	0.87	0.38	1.12	-0.74	0.97	0.11	1.14	-1.03
	ACC	1.20	1.91	1.00	0.91	1.20	1.87	1.00	0.87	1.26	1.72	1.01	0.71	1.17	1.87	0.98	0.89
	ACA	1.00	0.11	1.22	-1.11	1.01	0.12	1.21	-1.09	0.94	0.33	1.21	-0.88	1.06	0.12	1.24	-1.12
	ACG	0.85	1.88	0.65	1.23	0.88	1.89	0.67	1.22	0.93	1.58	0.67	0.91	0.81	1.90	0.65	1.25
Ala	GCU	0.92	0.15	1.16	-1.01	0.90	0.16	1.14	-0.98	0.85	1.21	1.14	0.07	0.95	0.16	1.17	-1.01
	GCC**	1.27	1.91	1.02	0.89	1.28	1.90	1.03	0.87	1.33	1.14	1.03	0.11	1.24	1.88	1.02	0.86
	GCA	0.81	0.14	1.06	-0.92	0.81	0.15	1.05	-0.90	0.75	0.66	1.04	-0.38	0.86	0.14	1.06	-0.92
	GCG	1.00	1.80	0.76	1.04	1.01	1.79	0.78	1.01	1.07	1.00	0.79	0.21	0.95	1.81	0.75	1.06
Tyr	UAU	0.81	0.05	1.00	-0.95	0.77	0.05	1.01	-0.96	0.72	0.2	0.99	-0.79	0.83	0.05	1.02	-0.97
	UAC**	1.19	1.95	1.00	0.95	1.23	1.95	0.99	0.96	1.28	1.80	1.01	0.79	1.17	1.95	0.98	0.97
His	CAU	0.93	0.12	1.09	-0.97	0.90	0.13	1.08	-0.95	0.84	0.95	1.07	-0.12	0.96	0.13	1.10	-0.97
	CAC	1.07	1.88	0.91	0.97	1.10	1.87	0.92	0.95	1.16	1.05	0.93	0.12	1.04	1.87	0.90	0.97
Gln	CAA	0.75	0.10	0.88	-0.78	0.73	0.11	0.88	-0.77	0.67	1.19	0.86	0.33	0.79	0.11	0.90	-0.79
	CAG*	1.25	1.90	1.12	0.78	1.27	1.89	1.12	0.77	1.33	0.81	1.14	-0.33	1.21	1.89	1.10	0.79
Asn	AAU	0.92	0.09	1.06	-0.97	0.90	0.10	1.06	-0.96	0.86	0.61	1.04	-0.43	0.95	0.11	1.06	-0.95
	AAC	1.08	1.91	0.94	0.97	1.10	1.90	0.94	0.96	1.14	1.39	0.96	0.43	1.05	1.89	0.94	0.95
Lys	AAA	0.65	0.09	0.79	-0.70	0.66	0.09	0.80	-0.71	0.62	0.25	0.79	-0.54	0.68	0.09	0.80	-0.71
	AAG**	1.35	1.91	1.21	0.70	1.34	1.91	1.2	0.71	1.38	1.75	1.21	0.54	1.32	1.91	1.20	0.71
Asp	GAU	0.96	0.12	1.15	-1.03	0.94	0.12	1.14	-1.02	0.89	0.77	1.14	-0.37	0.99	0.12	1.15	-1.03
	GAC	1.04	1.88	0.85	1.03	1.06	1.88	0.86	1.02	1.11	1.23	0.86	0.37	1.01	1.88	0.85	1.03
Glu	GAA	0.73	0.10	0.87	-0.77	0.73	0.12	0.88	-0.76	0.68	0.90	0.87	0.03	0.77	0.11	0.88	-0.77
	GAG*	1.27	1.90	1.13	0.77	1.27	1.88	1.12	0.76	1.32	1.10	1.13	-0.03	1.23	1.89	1.12	0.77
Cys	UGU	0.70	0.06	0.87	-0.81	0.67	0.06	0.86	-0.80	0.62	0.42	0.84	-0.42	0.72	0.06	0.87	-0.81
	UGC**	1.30	1.94	1.13	0.81	1.33	1.94	1.14	0.80	1.38	1.58	1.16	0.42	1.28	1.94	1.13	0.81
Arg	CGU	0.63	0.17	0.77	-0.60	0.62	0.18	0.77	-0.59	0.59	1.15	0.76	0.39	0.62	0.18	0.77	-0.59
	CGC**	1.42	2.86	1.10	1.76	1.43	2.79	1.11	1.68	1.53	1.92	1.11	0.81	1.35	2.78	1.10	1.68
	CGA	0.45	0.11	0.63	-0.52	0.46	0.12	0.64	-0.52	0.45	1.28	0.64	0.64	0.46	0.12	0.63	-0.51
	CGG	1.06	1.82	0.94	0.88	1.09	1.82	0.96	0.86	1.17	1.44	0.98	0.46	1.02	1.84	0.94	0.90
	AGA	1.00	0.09	1.19	-1.10	0.96	0.18	0.77	-0.59	0.87	0.06	1.15	-1.09	1.07	0.10	1.20	-1.10
	AGG	1.44	0.95	1.38	-0.43	1.45	2.79	1.11	1.68	1.39	0.15	1.35	-1.20	1.48	0.98	1.37	-0.39
Gly	GGU	0.83	0.17	1.02	-0.85	0.81	0.17	1.00	-0.83	0.77	0.67	0.98	-0.31	0.86	0.16	1.02	-0.86
	GGC**	1.52	2.67	1.10	1.57	1.53	2.65	1.13	1.52	1.59	1.57	1.13	0.44	1.47	2.65	1.10	1.55
	GGA	0.79	0.19	1.01	-0.82	0.79	0.20	1.02	-0.82	0.75	1.03	1.01	0.02	0.82	0.19	1.02	-0.83
	GGG	0.86	0.98	0.87	0.11	0.87	0.98	0.86	0.12	0.89	0.73	0.88	-0.15	0.86	0.99	0.86	0.13
Trp	UGG	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00
Met	AUG	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00	1.00	1.00	1.00	0.00
Ter	UAA	0.93	0.38	0.74	-0.36	0.66	0.42	0.73	-0.31	0.66	0.54	0.73	-0.19	0.67	0.38	0.73	-0.35
	UAG	0.93	0.90	0.90	0.00	0.93	0.92	0.91	0.01	0.92	0.50	0.89	-0.39	0.94	0.91	0.91	0.00
	UGA	1.42	1.00	1.00	0.00	1.41	1.00	1.00	0.00	1.43	1.96	1.38	0.58	1.39	1.70	1.35	0.35