Codon usage bias and its influencing factors in the whole genome of three truffles

doi:10.3969/j.issn.1004-1524.2022.07.11

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (7): 1439-1448.DOI: 10.3969/j.issn.1004-1524.2022.07.11

• Horticultural Science • Previous Articles Next Articles

Codon usage bias and its influencing factors in the whole genome of three truffles

HAN Lihong(), TIAN Xuelian, LIU Chao(), FU Xiaolin, WANG Yuanxian

Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, Yunnan, China

Received:2021-12-21 Online:2022-07-25 Published:2022-07-26
Contact: LIU Chao

Abstract

Abstract:

Truffle is a rare wild macrofungi for both medicine and food, it has high value in nutrition and health care. Codon bias analysis can provide a theoretical basis for genetic evolution and resource development of truffles. Based on the genomic data of Tuber melanosporum, T. magnatum and T. borchii, CodonW 1.4 2, Mega X software, and EMBOSS online website were used to systematically analyze the codon usage bias and influencing factors of the genomes of three truffles. The results showed that the codon usage patterns of the three truffles were highly similar, with a tendency to use the guanine or cytosine ending codons, and the effective number of codons showed high values. Among them, the similarity of codon usage between T. melanosporum and T. borchii was the highest. The guanine or cytosine (G/C) base related parameters of T. magnatum were higher than other two species. Among the optimal codons of the three truffles, the G/C ending codons accounted for 81.8%, 78.9% and 61.9% respectively. 24 high-frequency codons and 14 optimal codons were common in the three truffles. All of them prefer the guanine or cytosine or thymineas ending codons, but the preference was not strong as a whole. The results of Parity Rule 2 plot, ENC-plot, neutrality plot and correspondence analysis showed that the formation of codon bias of the three truffles were mainly affected by multiple factors such as selection pressure. Among them, T. melanosporum was mainly affected by translational selection pressure, and T. magnatum was mainly affected by other factors other than translational selection, and T. borchii was relatively less affected by selection pressure. The results showed that the codon use patterns of the three truffles were similar, and the codon usage bias was weak with low expression potential. The codon bias was mainly affected by multiple factors. The results provided a theoretical basis for species evolution and genetic breeding of truffles.

Key words: truffle, genome, codon usage bias, optimal codon, selection pressure

CLC Number:

S646

HAN Lihong, TIAN Xuelian, LIU Chao, FU Xiaolin, WANG Yuanxian. Codon usage bias and its influencing factors in the whole genome of three truffles[J]. Acta Agriculturae Zhejiangensis, 2022, 34(7): 1439-1448.

Figures/Tables 8

References 24

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参数Parameter	T3s/%	C3s/%	A3s/%	G3s/%	GC3s/%	GC/%	GC1/%	GC2/%	GC3/%	ENC
黑孢块菌 T. melanosporum	30.59 ±6.75 b	35.00 ±6.98 a	24.73 ±5.80 c	32.79 ±6.55 b	54.30 ±7.45 b	52.19 ±3.55 b	55.43 ±4.34 b	45.04 ±5.88 a	55.83 ±7.24 b	55.80 ±4.38 a
白块菌 T. magnatum	29.69 ±6.77 c	34.92 ±7.52 a	25.00 ±6.50 b	33.35 ±7.02 a	54.79 ±7.55 a	52.70 ±3.52 a	55.69 ±4.26 a	44.97 ±5.82 a	56.90 ±7.07 a	55.41 ±4.62 b
波氏块菌 T. borchii	31.24 ±7.04 a	32.65 ±7.21 b	27.81 ±6.52 a	30.86 ±7.38 c	51.11 ±7.23 c	51.27 ±3.67 c	54.62 ±4.91 c	44.74 ±5.94 b	53.45 ±6.83 c	55.69 ±4.58 a

参数Parameter	T3s/%	C3s/%	A3s/%	G3s/%	GC3s/%	GC/%	GC1/%	GC2/%	GC3/%	ENC
黑孢块菌 T. melanosporum	30.59 ±6.75 b	35.00 ±6.98 a	24.73 ±5.80 c	32.79 ±6.55 b	54.30 ±7.45 b	52.19 ±3.55 b	55.43 ±4.34 b	45.04 ±5.88 a	55.83 ±7.24 b	55.80 ±4.38 a
白块菌 T. magnatum	29.69 ±6.77 c	34.92 ±7.52 a	25.00 ±6.50 b	33.35 ±7.02 a	54.79 ±7.55 a	52.70 ±3.52 a	55.69 ±4.26 a	44.97 ±5.82 a	56.90 ±7.07 a	55.41 ±4.62 b
波氏块菌 T. borchii	31.24 ±7.04 a	32.65 ±7.21 b	27.81 ±6.52 a	30.86 ±7.38 c	51.11 ±7.23 c	51.27 ±3.67 c	54.62 ±4.91 c	44.74 ±5.94 b	53.45 ±6.83 c	55.69 ±4.58 a

氨基酸 Amino acid	密码子 Codon		黑孢块菌T. melanosporum						白块菌T. magnatum						波氏块菌T. borchii
氨基酸 Amino acid	密码子 Codon		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG	低表达 LEG
丙氨酸Ala	GCA		0.91		0.53		1.00		1.00		0.59		0.98		0.95		0.70	1.05
	GCC		1.07		1.55		1.00		1.05		1.58		1.05		1.05		1.29	1.02
	GCG		0.86		0.67		0.90		0.83		0.61		0.87		0.81		0.63	0.83
	GCT		1.16		1.25		1.10		1.12		1.23		1.09		1.18		1.37	1.10
半胱氨酸Cys	TGC		1.15		1.43		1.09		1.13		1.37		1.07		1.12		1.09	1.05
	TGT		0.85		0.57		0.91		0.87		0.63		0.93		0.88		0.91	0.95
天冬氨酸Asp	GAC		0.88		1.04		0.89		0.88		0.99		0.89		0.87		0.82	0.90
	GAT		1.12		0.96		1.11		1.12		1.01		1.11		1.13		1.18	1.10
谷氨酸Glu	GAA		0.83		0.59		0.89		0.93		0.64		0.86		0.87		0.77	0.92
	GAG		1.17		1.41		1.11		1.07		1.36		1.14		1.13		1.23	1.08
苯丙氨酸Phe	TTC		1.13		1.39		1.05		1.11		1.37		1.07		1.10		1.11	1.03
	TTT		0.87		0.61		0.95		0.89		0.63		0.93		0.90		0.89	0.97
甘氨酸Gly	GGA		0.98		0.84		1.03		1.18		0.98		1.03		1.01		1.03	1.02
	GGC		1.01		1.11		0.96		0.93		0.99		0.97		0.99		0.85	0.99
氨基酸 Amino acid		密码子 Codon		黑孢块菌T. melanosporum						白块菌T. magnatum						波氏块菌T. borchii
氨基酸 Amino acid		密码子 Codon		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome	高表达 HEG	低表达 LEG
		GGG		1.05		0.81		1.08		1.04		0.90		1.06		1.06	0.85	1.08
		GGT		0.96		1.24		0.94		0.84		1.13		0.94		0.94	1.28	0.91
组氨酸His		CAC		1.04		1.32		1.02		1.04		1.32		1.04		1.01	1.14	1.01
		CAT		0.96		0.68		0.98		0.96		0.68		0.96		0.99	0.86	0.99
异亮氨酸Ile		ATA		0.60		0.34		0.79		0.72		0.42		0.76		0.63	0.50	0.78
		ATC		1.28		1.66		1.12		1.19		1.57		1.15		1.23	1.27	1.14
		ATT		1.12		1.01		1.09		1.09		1.01		1.09		1.14	1.23	1.08
赖氨酸Lys		AAA		0.83		0.46		0.88		0.86		0.50		0.85		0.79	0.64	0.89
		AAG		1.17		1.54		1.12		1.14		1.50		1.15		1.21	1.36	1.11
亮氨酸Leu		CTA		0.71		0.40		0.83		0.81		0.41		0.79		0.78	0.52	0.87
		CTC		1.44		2.12		1.29		1.34		2.06		1.27		1.40	1.59	1.23
		CTG		0.94		0.84		0.94		0.95		0.86		1.05		0.88	0.70	0.94
		CTT		1.18		1.11		1.11		1.12		1.05		1.13		1.19	1.22	1.16
		TTA		0.52		0.36		0.69		0.62		0.24		0.66		0.58	0.51	0.72
		TTG		1.22		1.18		1.14		1.16		1.38		1.11		1.16	1.47	1.08
甲硫氨酸Met		ATG		1.00		1.00		1.00		1.00		1.00		1.00		1.00	1.00	1.00
天冬酰胺Asn		AAC		1.01		1.28		1.01		0.99		1.24		0.99		0.98	1.04	0.97
		AAT		0.99		0.72		0.99		1.01		0.76		1.01		1.02	0.96	1.03
脯氨酸Pro		CCA		1.05		0.76		1.12		1.08		0.75		0.98		1.10	0.92	1.10
		CCC		1.03		1.44		1.00		1.04		1.59		1.06		0.99	1.24	0.99
		CCG		0.92		0.82		0.94		0.89		0.71		0.99		0.85	0.57	0.89
		CCT		0.99		0.99		0.94		0.99		0.95		0.97		1.05	1.27	1.03
谷氨酰胺Gln		CAA		0.93		0.78		0.98		1.03		0.73		0.94		0.96	0.91	0.97
		CAG		1.07		1.22		1.02		0.97		1.27		1.06		1.04	1.09	1.03
精氨酸Arg		AGA		1.09		0.72		1.12		1.31		1.05		1.09		1.16	1.45	1.15
		AGG		1.45		1.44		1.23		1.31		1.67		1.30		1.43	1.70	1.26
		CGA		0.74		0.30		0.89		0.94		0.30		0.90		0.74	0.33	0.88
		CGC		1.06		1.70		1.00		0.91		1.42		0.96		1.04	1.03	0.93
		CGG		0.84		0.49		0.96		0.87		0.38		0.98		0.81	0.40	0.95
		CGT		0.82		1.36		0.79		0.66		1.18		0.77		0.82	1.10	0.83
丝氨酸Ser		AGC		1.00		1.05		0.97		1.05		1.05		1.05		1.00	0.78	1.00
		AGT		0.83		0.57		0.88		0.81		0.65		0.84		0.86	0.92	0.88
		TCA		0.88		0.54		0.99		1.00		0.57		0.94		0.91	0.78	0.99
		TCC		1.25		1.80		1.14		1.18		1.87		1.15		1.19	1.47	1.12
		TCG		0.92		0.71		0.96		0.88		0.64		1.02		0.85	0.48	0.92
		TCT		1.12		1.33		1.07		1.08		1.22		1.00		1.18	1.58	1.09
苏氨酸Thr		ACA		0.94		0.52		1.04		1.02		0.53		1.02		0.97	0.64	1.02
		ACC		1.30		1.90		1.17		1.21		1.92		1.19		1.25	1.60	1.15
		ACG		0.72		0.51		0.80		0.76		0.47		0.81		0.67	0.42	0.78
		ACT		1.04		1.07		0.99		1.02		1.07		0.99		1.11	1.33	1.05
缬氨酸Val		GTA		0.55		0.26		0.74		0.65		0.38		0.68		0.60	0.45	0.73
		GTC		1.15		1.66		1.04		1.09		1.49		1.10		1.12	1.20	1.06
		GTG		0.96		0.73		0.99		1.01		0.92		1.01		0.95	0.97	1.01
		GTT		1.33		1.35		1.23		1.26		1.20		1.20		1.33	1.38	1.21
色氨酸Trp		TGG		1.00		1.00		1.00		1.00		1.00		1.00		1.00	1.00	1.00
酪氨酸Tyr		TAC		1.12		1.34		1.08		1.05		1.37		1.10		1.08	1.08	1.02
		TAT		0.88		0.66		0.92		0.95		0.63		0.90		0.92	0.92	0.98
终止子Terminator		TAA		0.91		1.36		1.15		0.78		1.19		1.29		0.96	1.18	1.56
		TAG		1.11		0.99		1.52		0.84		1.14		1.30		1.07	1.07	1.44
		TGA		0.98		0.65		0.33		1.38		0.68		0.41		0.97	0.76	0

氨基酸 Amino acid	密码子 Codon		黑孢块菌T. melanosporum						白块菌T. magnatum						波氏块菌T. borchii
氨基酸 Amino acid	密码子 Codon		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG	低表达 LEG
丙氨酸Ala	GCA		0.91		0.53		1.00		1.00		0.59		0.98		0.95		0.70	1.05
	GCC		1.07		1.55		1.00		1.05		1.58		1.05		1.05		1.29	1.02
	GCG		0.86		0.67		0.90		0.83		0.61		0.87		0.81		0.63	0.83
	GCT		1.16		1.25		1.10		1.12		1.23		1.09		1.18		1.37	1.10
半胱氨酸Cys	TGC		1.15		1.43		1.09		1.13		1.37		1.07		1.12		1.09	1.05
	TGT		0.85		0.57		0.91		0.87		0.63		0.93		0.88		0.91	0.95
天冬氨酸Asp	GAC		0.88		1.04		0.89		0.88		0.99		0.89		0.87		0.82	0.90
	GAT		1.12		0.96		1.11		1.12		1.01		1.11		1.13		1.18	1.10
谷氨酸Glu	GAA		0.83		0.59		0.89		0.93		0.64		0.86		0.87		0.77	0.92
	GAG		1.17		1.41		1.11		1.07		1.36		1.14		1.13		1.23	1.08
苯丙氨酸Phe	TTC		1.13		1.39		1.05		1.11		1.37		1.07		1.10		1.11	1.03
	TTT		0.87		0.61		0.95		0.89		0.63		0.93		0.90		0.89	0.97
甘氨酸Gly	GGA		0.98		0.84		1.03		1.18		0.98		1.03		1.01		1.03	1.02
	GGC		1.01		1.11		0.96		0.93		0.99		0.97		0.99		0.85	0.99
氨基酸 Amino acid		密码子 Codon		黑孢块菌T. melanosporum						白块菌T. magnatum						波氏块菌T. borchii
氨基酸 Amino acid		密码子 Codon		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome		高表达 HEG		低表达 LEG		基因组 Genome	高表达 HEG	低表达 LEG
		GGG		1.05		0.81		1.08		1.04		0.90		1.06		1.06	0.85	1.08
		GGT		0.96		1.24		0.94		0.84		1.13		0.94		0.94	1.28	0.91
组氨酸His		CAC		1.04		1.32		1.02		1.04		1.32		1.04		1.01	1.14	1.01
		CAT		0.96		0.68		0.98		0.96		0.68		0.96		0.99	0.86	0.99
异亮氨酸Ile		ATA		0.60		0.34		0.79		0.72		0.42		0.76		0.63	0.50	0.78
		ATC		1.28		1.66		1.12		1.19		1.57		1.15		1.23	1.27	1.14
		ATT		1.12		1.01		1.09		1.09		1.01		1.09		1.14	1.23	1.08
赖氨酸Lys		AAA		0.83		0.46		0.88		0.86		0.50		0.85		0.79	0.64	0.89
		AAG		1.17		1.54		1.12		1.14		1.50		1.15		1.21	1.36	1.11
亮氨酸Leu		CTA		0.71		0.40		0.83		0.81		0.41		0.79		0.78	0.52	0.87
		CTC		1.44		2.12		1.29		1.34		2.06		1.27		1.40	1.59	1.23
		CTG		0.94		0.84		0.94		0.95		0.86		1.05		0.88	0.70	0.94
		CTT		1.18		1.11		1.11		1.12		1.05		1.13		1.19	1.22	1.16
		TTA		0.52		0.36		0.69		0.62		0.24		0.66		0.58	0.51	0.72
		TTG		1.22		1.18		1.14		1.16		1.38		1.11		1.16	1.47	1.08
甲硫氨酸Met		ATG		1.00		1.00		1.00		1.00		1.00		1.00		1.00	1.00	1.00
天冬酰胺Asn		AAC		1.01		1.28		1.01		0.99		1.24		0.99		0.98	1.04	0.97
		AAT		0.99		0.72		0.99		1.01		0.76		1.01		1.02	0.96	1.03
脯氨酸Pro		CCA		1.05		0.76		1.12		1.08		0.75		0.98		1.10	0.92	1.10
		CCC		1.03		1.44		1.00		1.04		1.59		1.06		0.99	1.24	0.99
		CCG		0.92		0.82		0.94		0.89		0.71		0.99		0.85	0.57	0.89
		CCT		0.99		0.99		0.94		0.99		0.95		0.97		1.05	1.27	1.03
谷氨酰胺Gln		CAA		0.93		0.78		0.98		1.03		0.73		0.94		0.96	0.91	0.97
		CAG		1.07		1.22		1.02		0.97		1.27		1.06		1.04	1.09	1.03
精氨酸Arg		AGA		1.09		0.72		1.12		1.31		1.05		1.09		1.16	1.45	1.15
		AGG		1.45		1.44		1.23		1.31		1.67		1.30		1.43	1.70	1.26
		CGA		0.74		0.30		0.89		0.94		0.30		0.90		0.74	0.33	0.88
		CGC		1.06		1.70		1.00		0.91		1.42		0.96		1.04	1.03	0.93
		CGG		0.84		0.49		0.96		0.87		0.38		0.98		0.81	0.40	0.95
		CGT		0.82		1.36		0.79		0.66		1.18		0.77		0.82	1.10	0.83
丝氨酸Ser		AGC		1.00		1.05		0.97		1.05		1.05		1.05		1.00	0.78	1.00
		AGT		0.83		0.57		0.88		0.81		0.65		0.84		0.86	0.92	0.88
		TCA		0.88		0.54		0.99		1.00		0.57		0.94		0.91	0.78	0.99
		TCC		1.25		1.80		1.14		1.18		1.87		1.15		1.19	1.47	1.12
		TCG		0.92		0.71		0.96		0.88		0.64		1.02		0.85	0.48	0.92
		TCT		1.12		1.33		1.07		1.08		1.22		1.00		1.18	1.58	1.09
苏氨酸Thr		ACA		0.94		0.52		1.04		1.02		0.53		1.02		0.97	0.64	1.02
		ACC		1.30		1.90		1.17		1.21		1.92		1.19		1.25	1.60	1.15
		ACG		0.72		0.51		0.80		0.76		0.47		0.81		0.67	0.42	0.78
		ACT		1.04		1.07		0.99		1.02		1.07		0.99		1.11	1.33	1.05
缬氨酸Val		GTA		0.55		0.26		0.74		0.65		0.38		0.68		0.60	0.45	0.73
		GTC		1.15		1.66		1.04		1.09		1.49		1.10		1.12	1.20	1.06
		GTG		0.96		0.73		0.99		1.01		0.92		1.01		0.95	0.97	1.01
		GTT		1.33		1.35		1.23		1.26		1.20		1.20		1.33	1.38	1.21
色氨酸Trp		TGG		1.00		1.00		1.00		1.00		1.00		1.00		1.00	1.00	1.00
酪氨酸Tyr		TAC		1.12		1.34		1.08		1.05		1.37		1.10		1.08	1.08	1.02
		TAT		0.88		0.66		0.92		0.95		0.63		0.90		0.92	0.92	0.98
终止子Terminator		TAA		0.91		1.36		1.15		0.78		1.19		1.29		0.96	1.18	1.56
		TAG		1.11		0.99		1.52		0.84		1.14		1.30		1.07	1.07	1.44
		TGA		0.98		0.65		0.33		1.38		0.68		0.41		0.97	0.76	0

物种Species	坐标轴Axis	GC3s	GC	ENC	Fop
黑孢块菌T. melanosporum	Axis1	0.899^**	0.712^**	-0.238^**	0.241^**
	Axis2	-0.302^**	-0.154^**	0.562^**	-0.668^**
白块菌T. magnatum	Axis1	-0.804^**	-0.559^**	0.393^**	-0.702^**
	Axis2	0.500^**	0.353^**	0.032^**	-0.287^**
波氏块菌T. borchii	Axis1	-0.008	-0.035^**	0.225^**	-0.637^**
	Axis2	0.935^**	0.611^**	-0.109^**	0.339^**

Codon usage bias and its influencing factors in the whole genome of three truffles

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