Analysis of Chloroplast Genome Characteristics and Codon Usage Bias of Fissisfigma polyanthum Merr.

doi:10.13304/j.nykjdb.2022.0114

Abstract

Abstract:

To study the structure characteristics， phylogeny and codon usage bias ofchloroplast genome in Fissisfigma polyanthum Merr.， the chloroplast genome of Fissisfigma polyanthum Merr. wassequenced and analyzed. The results showed that the chloroplast genome was composed of large single-copy region， small single-copy region and a pair of reverse repeat regions. The total length was 189 920 bp， which included 118 genes （99 genes encoding protein， 11 tRNA genes and 8 ribosome rRNA genes）， and 71 simple sequence repeats （SSRs） were also identified. The phylogenetic analysis showed that F. polyanthum Merr. was closely related to Annona muricata. The codon preference analysis showed that the codon usage bias of F. polyanthum Merr. was weak， and the codon preference was mainly affected by selection factor. Finally， 11 optimal codes were selected， 10 of which ended with A/U. These results provided scientific basis for phylogeny and construction of expression vector of F. polyanthum Merr.

Key words: Fissisfigma polyanthum Merr., chloroplast genome, characteristics, codon usage bias

摘要：

为探究老班瑶药牛耳风叶绿体基因组的结构特征、系统进化以及密码子偏好性，以瑶药牛耳风为研究材料，对其叶绿体基因组进行测序和组装。结果表明，牛耳风叶绿体基因组由大单拷贝区、小单拷贝区以及1对反向重复区组成，全长189 920 bp，包含118个基因，其中99个编码蛋白质的基因，11个tRNA基因，8个核糖体rRNA基因；共检测到71个简单序列重复（simple sequence repeat， SSR）位点。系统进化分析表明牛耳风与番荔枝属的刺果番荔枝（Annona muricata）亲缘关系最近。密码子偏好性分析表明，牛耳风的密码子偏好性较弱，且密码子偏好性主要受选择因素的影响，最终选出11个最优密码子，其中10个以A/U结尾，为瑶药牛耳风的系统进化研究等提供科学依据。

关键词: 牛耳风, 叶绿体基因组, 特征, 密码子偏好性

CLC Number:

Qiwei YAN, Xianglan LIANG, Qiuyun TAO, Qiuxiang LUO, Song GUO. Analysis of Chloroplast Genome Characteristics and Codon Usage Bias of Fissisfigma polyanthum Merr.[J]. Journal of Agricultural Science and Technology, 2022, 24(8): 74-86.

严其伟, 梁湘兰, 陶秋云, 罗秋香, 郭松. 老班瑶药牛耳风叶绿体基因组特征及其密码子使用偏好性分析[J]. 中国农业科技导报, 2022, 24(8): 74-86.

Figures/Tables 14

References 26

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核苷酸类型 Nucleotide type	简单重复序列 Simple sequence repeat	重复序列个数 Number of SSR
单核苷酸 Mononucleotide	A	25
	C	1
	T	23
二核苷酸 Dinucleotide	AT	2
三核苷酸 Trinucleotide	AAG	1
	AAT	2
	ATA	1
	ATT	2
	CTT	2
	GAA	1
	GAT	1
	TAT	1
四核苷酸 Tetranucleotide	AAGT	1
	ATAG	1
	GAAC	1
	TATT	1
	TTCA	1
五核苷酸 Pentanucleotide	TATATC	1
六核苷酸 Hexanucleotide	CAGAGT	1
	CTCTGA	1
	TATATC	1

核苷酸类型 Nucleotide type	简单重复序列 Simple sequence repeat	重复序列个数 Number of SSR
单核苷酸 Mononucleotide	A	25
	C	1
	T	23
二核苷酸 Dinucleotide	AT	2
三核苷酸 Trinucleotide	AAG	1
	AAT	2
	ATA	1
	ATT	2
	CTT	2
	GAA	1
	GAT	1
	TAT	1
四核苷酸 Tetranucleotide	AAGT	1
	ATAG	1
	GAAC	1
	TATT	1
	TTCA	1
五核苷酸 Pentanucleotide	TATATC	1
六核苷酸 Hexanucleotide	CAGAGT	1
	CTCTGA	1
	TATATC	1

基因 Gene	GC含量 GC content/%				有效密码子数 ENC
基因 Gene	第1密码子 GC₁	第2密码子 GC₂	第3密码子 GC₃	平均 GC_all	有效密码子数 ENC
rps12	50.42	52.10	28.57	43.70	45.427
ndhF	38.38	37.30	29.05	34.91	49.090
ccsA	35.19	39.81	32.72	35.91	55.085
ndhD	41.20	38.60	30.20	36.67	49.432
ndhE	37.25	36.27	29.41	34.31	44.837
ndhG	44.63	35.03	26.55	35.40	47.921
ndhI	42.08	38.25	27.87	36.07	50.444
ndhA	46.43	41.21	25.82	37.82	46.075
ndhH	52.28	36.80	31.98	40.36	53.004
rps7	49.36	42.95	22.44	38.25	49.808
ndhB	42.27	39.14	32.88	38.10	47.965
rpl22	42.96	42.25	36.62	40.61	54.629
rps3	45.91	32.27	25.91	34.70	48.708
rpl16	51.47	51.47	34.56	45.83	39.393
rpl14	56.10	35.77	27.64	39.84	46.735
rps8	42.86	41.35	30.83	38.35	48.660
infA	48.41	23.02	25.40	32.28	49.830
rps11	53.69	58.39	24.16	45.41	55.674
rpoA	48.90	31.97	31.03	37.30	56.990
petB	48.13	41.12	33.64	40.97	44.890
psbB	54.42	45.78	36.15	45.45	52.419
rpl20	41.53	50.00	36.44	42.66	44.510
rps18	43.68	38.51	36.78	39.66	55.256
petA	53.89	34.89	33.96	40.91	52.314

基因 Gene	GC含量 GC content/%				有效密码子数 ENC
基因 Gene	第1密码子 GC₁	第2密码子 GC₂	第3密码子 GC₃	平均 GC_all	有效密码子数 ENC
rps12	50.42	52.10	28.57	43.70	45.427
ndhF	38.38	37.30	29.05	34.91	49.090
ccsA	35.19	39.81	32.72	35.91	55.085
ndhD	41.20	38.60	30.20	36.67	49.432
ndhE	37.25	36.27	29.41	34.31	44.837
ndhG	44.63	35.03	26.55	35.40	47.921
ndhI	42.08	38.25	27.87	36.07	50.444
ndhA	46.43	41.21	25.82	37.82	46.075
ndhH	52.28	36.80	31.98	40.36	53.004
rps7	49.36	42.95	22.44	38.25	49.808
ndhB	42.27	39.14	32.88	38.10	47.965
rpl22	42.96	42.25	36.62	40.61	54.629
rps3	45.91	32.27	25.91	34.70	48.708
rpl16	51.47	51.47	34.56	45.83	39.393
rpl14	56.10	35.77	27.64	39.84	46.735
rps8	42.86	41.35	30.83	38.35	48.660
infA	48.41	23.02	25.40	32.28	49.830
rps11	53.69	58.39	24.16	45.41	55.674
rpoA	48.90	31.97	31.03	37.30	56.990
petB	48.13	41.12	33.64	40.97	44.890
psbB	54.42	45.78	36.15	45.45	52.419
rpl20	41.53	50.00	36.44	42.66	44.510
rps18	43.68	38.51	36.78	39.66	55.256
petA	53.89	34.89	33.96	40.91	52.314

氨基酸 Amino acid	密码子 Codon	数量 Number	相对使用度RSCU	氨基酸 Amino acid	密码子 Codon	数量 Number	相对使用度RSCU
苯丙氨酸 Phe	UUU	539	1.23	酪氨酸 Tyr	UAU	479	1.59
苯丙氨酸 Phe	UUC	334	0.77	酪氨酸 Tyr	UAC	123	0.41
亮氨酸 Leu	UUA	507	1.80	组氨酸 His	CAU	318	1.50
	UUG	361	1.28	组氨酸 His	CAC	107	0.50
	CUU	344	1.22	谷氨酰胺 Gln	CAA	412	1.43
	CUC	120	0.43	谷氨酰胺 Gln	CAG	166	0.57
	CUA	246	0.87	天冬酰胺 Asn	AAU	471	1.50
	CUG	112	0.40	天冬酰胺 Asn	AAC	159	0.50
缬氨酸 Val	GUU	342	1.40	赖氨酸 Lys	AAA	558	1.51
	GUC	128	0.53	赖氨酸 Lys	AAG	181	0.49
	GUA	354	1.45	天冬氨酸 Asp	GAU	474	1.56
	GUG	150	0.62	天冬氨酸 Asp	GAC	135	0.44
丝氨酸 Ser	UCU	330	1.70	谷氨酸 Glu	GAA	610	1.46
	UCC	192	0.99	谷氨酸 Glu	GAG	224	0.54
	UCA	210	1.08	半胱氨酸 Cys	UGU	136	1.50
	UCG	130	0.67	半胱氨酸 Cys	UGC	45	0.50
	AGU	218	1.13	精氨酸 Arg	CGU	229	1.35
	AGC	82	0.42		CGC	78	0.46
脯氨酸 Pro	CCU	253	1.44		CGA	231	1.36
	CCC	170	0.97		CGG	82	0.48
	CCA	203	1.16		AGA	285	1.68
	CCG	75	0.43		AGG	114	0.67
苏氨酸 Thr	ACU	343	1.63	甘氨酸 Gly	GGU	405	1.29
	ACC	166	0.79		GGC	150	0.48
	ACA	235	1.11		GGA	489	1.56
	ACG	100	0.47		GGG	209	0.67
丙氨酸 Ala	GCU	460	1.76	异亮氨酸 Ile	AUU	675	1.46
	GCC	181	0.69		AUC	299	0.65
	GCA	266	1.02		AUA	413	0.89
	GCG	136	0.52