Genomic Characteristics and Codon Preference Analysis of Schefflera octophylla （Lour.） Harms Chloroplasts

doi:10.13304/j.nykjdb.2023.0006

Abstract

Abstract:

To study the genetic structure and function， genetic codon preference， influencing factors and optimal codon of Schefflera octophylla， the Schefflera octophylla （Lour.） Harms was used as research material. The full sequence of the chloroplast genome was sequenced and assembled. The results showed that the chloroplast genome of S. octophylla was consist of a large single copy region， a small single copy region and 2 reverse repeat regions， with a total length of 156 532 bp， and 123 functional genes were obtained including 8 ribosomal rRNA genes， 29 tRNA genes and 86 protein coding genes. A total of 84 SSR loci were detected. The preference analysis of codons showed that the optimal codons of S. octophylla chloroplast genomic codons tended to end in A/U bases， which indicated natural selection was main factor of preference analysis of codons. Phylogenetic analysis showed that S. actophylla had closely related to Kalopanax septemlobus. Above results provided scientific basis for the study and application of chloroplast genome of S. octophylla.

Key words: Schefflera octophylla （Lour.） Harms, chloroplast genome, codon preference, optimal code

摘要：

为探究老班瑶药鸭脚风叶绿体基因组的结构特征、系统进化以及密码子偏好性，以瑶药鸭脚风为研究材料，对瑶药鸭脚风叶绿体基因组进行测序和组装。结果表明，鸭脚风的叶绿体基因组由大单拷贝区、小单拷贝区以及2个反向重复区组成，全长156 532 bp，包含123个基因，分别为8个核糖体rRNA基因、29个转录tRNA基因和86个蛋白质编码基因。共检测到84个SSR位点。密码子偏好性分析显示，鸭脚风的叶绿体基因最优密码子偏好以A/U碱基结尾，自然选择可能是其密码子使用模式的主要影响因素。系统进化分析表明，鸭脚风与辐叶鹅掌柴亲缘关系密切。以上研究结果为鸭脚风叶绿体基因组研究和应用提供了科学依据。

关键词: 鸭脚风, 叶绿体基因组, 密码子偏好性, 最优密码子

CLC Number:

Q949.95

Chunlian LI, Peng ZHANG, Chuping CAI, Shuifeng QIN, Shanfang XIAO, Qiuxiang LUO, Song GUO, Junfeng LAN. Genomic Characteristics and Codon Preference Analysis of Schefflera octophylla （Lour.） Harms Chloroplasts[J]. Journal of Agricultural Science and Technology, 2024, 26(12): 63-76.

李春连, 张鹏, 蔡楚平, 覃水凤, 肖善芳, 罗秋香, 郭松, 蓝峻峰. 瑶药鸭脚风叶绿体基因组结构解析及密码子偏好性分析[J]. 中国农业科技导报, 2024, 26(12): 63-76.

Figures/Tables 13

References 28

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区域 Region	含量 Content/%					长度 Length/bp
区域 Region	A	T	C	G	GC	长度 Length/bp
反向重复区a IR a	31.13	30.15	19.03	19.70	38.73	13 929
反向重复区b IR b	30.15	31.13	19.69	19.03	38.72	13 929
大单拷贝区LSC	31.38	32.51	18.49	17.62	36.11	86 593
小单拷贝区SSC	29.53	29.33	20.92	20.22	41.13	42 081
总计Total	30.55	30.77	19.53	19.14	38.67	156 532

区域 Region	含量 Content/%					长度 Length/bp
区域 Region	A	T	C	G	GC	长度 Length/bp
反向重复区a IR a	31.13	30.15	19.03	19.70	38.73	13 929
反向重复区b IR b	30.15	31.13	19.69	19.03	38.72	13 929
大单拷贝区LSC	31.38	32.51	18.49	17.62	36.11	86 593
小单拷贝区SSC	29.53	29.33	20.92	20.22	41.13	42 081
总计Total	30.55	30.77	19.53	19.14	38.67	156 532

基序类型 Motif type	基序 Motif	数量 Number
单核苷酸 Mononucleotide	A	20
	C	2
	G	2
	T	18
二核苷酸 Dinucleotide	AT	6
二核苷酸 Dinucleotide	TA	10
三核苷酸 Trinucleotide	ATA	2
三核苷酸 Trinucleotide	TTC	2
四核苷酸 Tetranucleotide	AAAG	2
	AAGA	2
	AATT	2
	AGGT	2
	CTAC	2
	TATT	2
	TCTT	2
五核苷酸 Pentanucleotide	ATTAG	2
	CTAAT	2
	TAATA	2
	TATTA	2

基序类型 Motif type	基序 Motif	数量 Number
单核苷酸 Mononucleotide	A	20
	C	2
	G	2
	T	18
二核苷酸 Dinucleotide	AT	6
二核苷酸 Dinucleotide	TA	10
三核苷酸 Trinucleotide	ATA	2
三核苷酸 Trinucleotide	TTC	2
四核苷酸 Tetranucleotide	AAAG	2
	AAGA	2
	AATT	2
	AGGT	2
	CTAC	2
	TATT	2
	TCTT	2
五核苷酸 Pentanucleotide	ATTAG	2
	CTAAT	2
	TAATA	2
	TATTA	2

基因Gene	GC₁/%	GC₂/%	GC₃/%	GC_all/%	有效密码子数ENC
ycf4	45.41	41.62	34.05	40.36	54.543
ycf3	48.24	38.82	31.18	39.41	53.137
ycf2	41.71	35.24	36.51	37.82	52.871
ycf1	36.25	28.81	24.14	29.73	45.425
rps18	38.53	40.37	23.85	34.25	43.502
rps14	43.56	49.50	36.63	43.23	45.428
rps12	50.34	48.28	35.86	44.83	53.428
rps11	54.68	57.55	29.50	47.24	51.675
rps8	40.74	38.52	23.70	34.32	56.138
rps7	53.21	45.51	23.08	40.60	45.032
rps4	51.49	38.61	29.70	39.93	53.819
rps3	47.27	33.18	25.91	35.45	50.951
rps2	41.77	41.35	30.80	37.97	47.389
rpoC2	46.76	36.96	30.91	38.21	50.736
rpoC1	50.65	37.63	27.93	38.74	50.485
rpoB	51.07	38.19	28.76	39.34	49.289
rpoA	46.45	34.32	28.40	36.39	51.196
rpl22	41.46	37.89	25.47	34.99	47.832
rpl20	40.31	42.64	24.81	35.92	45.668
rpl16	51.67	50.83	20.00	40.83	37.621
rpl14	56.10	38.21	30.08	41.46	48.896
rpl2	51.04	47.57	32.64	43.75	53.656
rbcL	59.03	43.49	31.30	44.61	49.622
psbD	51.69	43.22	31.64	42.18	44.743
psbC	52.95	46.20	32.28	43.81	45.479
psbB	55.01	46.17	55.01	43.94	46.223
psbA	50.28	43.79	34.46	42.84	41.646
psaB	48.71	43.13	31.84	41.23	48.158
psaA	52.73	43.41	32.36	42.83	49.982
petD	48.57	40.57	28.57	39.24	42.235
petB	49.54	41.28	28.44	39.76	43.486
PetA	52.34	36.76	31.15	40.08	51.579
ndhK	44.69	44.69	28.32	39.23	51.351
ndhJ	50.94	37.74	31.45	40.04	50.063
ndhI	42.86	36.31	29.76	36.31	44.478
ndhH	51.27	36.80	28.43	38.83	49.105
ndhG	45.76	35.03	24.86	35.22	49.114
NdhF	36.56	35.22	24.73	32.17	44.234
ndhE	40.20	34.31	24.51	33.01	40.348
ndhD	41.75	37.68	30.35	36.59	47.868
ndhC	45.45	33.06	26.45	34.99	44.721
ndhB	41.68	38.16	32.29	37.38	48.175
ndhA	41.56	35.82	26.41	34.60	47.875
matK	39.92	33.00	29.84	34.26	51.225
clpP	57.14	38.27	31.12	42.18	49.916
cemA	40.00	29.13	29.57	32.90	45.567
ccsA	33.54	37.89	23.60	31.68	46.626
atpI	49.19	37.90	28.63	38.58	46.754
atpF	46.60	32.52	36.41	38.51	50.072
atpE	50.35	39.01	32.62	40.66	54.058
atpB	55.71	41.68	30.06	42.48	48.621
atpA	56.69	40.16	26.38	41.08	48.114
accD	41.18	34.90	31.37	35.82	48.775
平均Mean	47.22	39.60	29.78	38.71	48.282