Comparative Analysis of Chloroplast Genomes from Rubuspoliophyllus and Rubus yunanicus

doi:10.19586/j.2095-2341.2023.0133

Current Biotechnology ›› 2024, Vol. 14 ›› Issue (2): 237-247.DOI: 10.19586/j.2095-2341.2023.0133

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Comparative Analysis of Chloroplast Genomes from Rubuspoliophyllus and Rubus yunanicus

Kang HU¹^,²(), Liping YU¹^,², Wei GU¹, Zhimin HE¹^,², Junxin ZHANG¹^,², Zixuan LIU¹^,², Tiran HUANG¹^,²^,³(), Mingfeng YANG¹^,²()

^1.College of Biological and Resource Environment，Beijing University of Agriculture，Beijing 102206，China
^2.Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs，Beijing University of Agriculture，Beijing 102206，China
^3.College of Life Sciences，University of Chinese Academy of Sciences，Beijing 100049，China

Received:2023-10-23 Accepted:2023-11-29 Online:2024-03-25 Published:2024-04-17
Contact: Tiran HUANG,Mingfeng YANG

毛叶悬钩子和云南悬钩子叶绿体基因组比较分析

胡康¹^,²(), 于丽平¹^,², 谷薇¹, 贺志敏¹^,², 张峻鑫¹^,², 刘子璇¹^,², 黄体冉¹^,²^,³(), 杨明峰¹^,²()

^1.北京农学院生物与资源环境学院，北京 102206
^2.北京农学院，农业农村部华北都市农业重点实验室，北京 102206
^3.中国科学院大学生命科学学院，北京 100049

通讯作者: 黄体冉,杨明峰
作者简介:胡康 E-mail: gan9933@163.com
基金资助:
北京市属高等学校高水平教学创新团队建设支持计划项目(BPHR20220211);北京农学院2020年和2021年本科生科研训练项目

Abstract

Abstract:

Rubuspoliophyllus and R.yunanicus belong to the Rubus subsect. Acuminati（Focke）T.T.Yu & L.T.Lu of Rosaceae. They have similar morphological characteristics and geographical distribution. So it is difficult to distinguish them only by morphological characteristics. In this study， their chloroplast genome sequence were obtained by high-throughput sequencing technology of Illumina， and the sequences were filtered， assembled， annotated and analyzed. Then the phylogenetic tree based on chloroplast genome sequence was constructed. The results showed that the complete chloroplast genomes size of R. poliophyllus and R. yunanicus were 156 298 bp and 156 299 bp， and the GC content of the two species was 37.2%. One hundred and fifty-nine chloroplast genes were detected， including 104 protein-coding genes， 45 tRNA genes and 10 rRNA genes respectively. The number of palindromic repeats， direct repeats， reverse repeats between R. poliophyllus and R. yunanicus were 17， 17； 19， 17； 4， 3， respectively. There were 32 codons with relative synonymous codon usage （RSCU）>1.00 in the these two species. The codon preference ended with A/U， and the effective number of codons were greater than 45. Phylogenetic analysis based on the chloroplast geneme and the rpoC1-rpoB gene sequence showed that R. poliophyllus and R. yunanicus were clustered into the same clade， which indicated that they had a closely genetic relationships. This study will provide a theoretical basis for the molecular identification， genetic diversity and phylogenetic relationships of R. poliophyllus and R. yunanicus.

Key words: Rubus poliophyllus, Rubus yunanicus, chloroplast genome, codon bias, phylogenetic analysis

摘要：

毛叶悬钩子(Rubus poliophyllus)和云南悬钩子(Rubus yunanicus)隶属于蔷薇科（Rosaceae）悬钩子属（Rubus）的尖叶亚组（Subsect. Acuminati），二者的形态特征和地理分布较为相似，因此难以分辨。通过Illumina高通量测序技术得到了二者的叶绿体基因组序列，并对序列进行过滤、组装、注释和分析，构建了基于叶绿体基因组序列的系统发育树。结果表明，毛叶悬钩子和云南悬钩子的基因组全长分别为156 298 bp和156 299 bp，基因组序列总GC含量均为37.2%。均检测到159个叶绿体基因，其中蛋白质编码基因104个，tRNA 基因45个，rRNA 基因10个。毛叶悬钩子和云南悬钩子均含有17个回文重复序列，正向重复序列个数分别为19、17，反向重复序列分别为4、3。二者的同义密码子使用度（relative synonymous codon usage，RSCU）>1.00的密码子均有32个，密码子偏好以A/U结尾，有效密码子数均大于45。根据叶绿体全基因组及筛选到的rpoC1-rpoB基因序列所构建的系统发育树显示，毛叶悬钩子和云南悬钩子均聚为同一个分支，表明二者具有较近的亲缘关系。研究结果可为毛叶悬钩子和云南悬钩子的物种分子鉴定、遗传多样性研究及其系统发育关系提供理论依据。

关键词: 毛叶悬钩子, 云南悬钩子, 叶绿体基因组, 密码子偏好性, 系统发育

CLC Number:

Q812

Kang HU, Liping YU, Wei GU, Zhimin HE, Junxin ZHANG, Zixuan LIU, Tiran HUANG, Mingfeng YANG. Comparative Analysis of Chloroplast Genomes from Rubuspoliophyllus and Rubus yunanicus[J]. Current Biotechnology, 2024, 14(2): 237-247.

胡康, 于丽平, 谷薇, 贺志敏, 张峻鑫, 刘子璇, 黄体冉, 杨明峰. 毛叶悬钩子和云南悬钩子叶绿体基因组比较分析[J]. 生物技术进展, 2024, 14(2): 237-247.

Figures/Tables 13

References 23

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物种	长度/bp				GC含量/%					rRNA	tRNA	内含子基因	编码序列
物种	Cp	LSC	SSC	IRa	IRb	Cp	LSC	SSC	IR	rRNA	tRNA	内含子基因	编码序列
毛叶悬钩子(R. poliophyllus)	156 298	85 894	18 850	25 777	25 777	37.2	35.1	31.2	42.8	10	45	27	104
云南悬钩子(R. yunanicus)	156 299	85 896	18 849	25 777	25 777	37.2	35.1	31.2	42.8	10	45	27	104
高粱泡(R. lambertianus)	156 316	85 879	18 873	25 782	25 782	37.2	35.1	31.2	42.8	10	45	27	104
高粱泡变种(R. lambertianus var.)	156 569	86 123	18 874	25 782	28 790	37.2	35.1	31.2	42.8	10	45	27	104
蛇泡筋(R. cochinchinensis)	156 240	85 850	18 848	25 771	25 771	37.2	35.1	31.2	42.8	10	45	27	104

物种	长度/bp				GC含量/%					rRNA	tRNA	内含子基因	编码序列
物种	Cp	LSC	SSC	IRa	IRb	Cp	LSC	SSC	IR	rRNA	tRNA	内含子基因	编码序列
毛叶悬钩子(R. poliophyllus)	156 298	85 894	18 850	25 777	25 777	37.2	35.1	31.2	42.8	10	45	27	104
云南悬钩子(R. yunanicus)	156 299	85 896	18 849	25 777	25 777	37.2	35.1	31.2	42.8	10	45	27	104
高粱泡(R. lambertianus)	156 316	85 879	18 873	25 782	25 782	37.2	35.1	31.2	42.8	10	45	27	104
高粱泡变种(R. lambertianus var.)	156 569	86 123	18 874	25 782	28 790	37.2	35.1	31.2	42.8	10	45	27	104
蛇泡筋(R. cochinchinensis)	156 240	85 850	18 848	25 771	25 771	37.2	35.1	31.2	42.8	10	45	27	104

物种	GeneBank ID	GC/%	GC1/%	GC2/%	GC3/%	ENC
毛叶悬钩子(R. poliophyllus)	PE01833328	37.75	45.50	37.23	30.53	50.20
云南悬钩子(R. yunanicus)	HTR285	37.77	45.43	37.39	30.49	50.20
高粱泡(R. lambertianus)	NC_056931.1	37.78	45.44	37.42	30.48	50.17
蛇泡筋(R. cochinchinensis)	HTR451	37.78	45.44	37.44	30.48	50.19

物种	GeneBank ID	GC/%	GC1/%	GC2/%	GC3/%	ENC
毛叶悬钩子(R. poliophyllus)	PE01833328	37.75	45.50	37.23	30.53	50.20
云南悬钩子(R. yunanicus)	HTR285	37.77	45.43	37.39	30.49	50.20
高粱泡(R. lambertianus)	NC_056931.1	37.78	45.44	37.42	30.48	50.17
蛇泡筋(R. cochinchinensis)	HTR451	37.78	45.44	37.44	30.48	50.19

氨基酸	密码子	数目	RSCU	氨基酸	密码子	数目	RSCU	氨基酸	密码子	数目	RSCU
苯丙氨酸	UUU	842	1.38	丝氨酸	UCU	473	1.54		AGA	421	1.61
	UUC	465	0.62		UCC	309	1.01		AGG	148	0.51
亮氨酸	UUA	752	2.05		UCA	339	1.07	酪氨酸	UAU	673	1.57
	UUG	485	1.20		UCG	182	0.66		UAC	170	0.36
	CUU	534	1.33		AGU	322	1.34	终止密码子	UAA	28	1.50
	CUC	160	0.33		AGC	102	0.38		UAG	18	0.96
	CUA	313	0.69	脯氨酸	CCU	349	1.40		UGA	10	0.54
	CUG	163	0.40		CCC	183	0.69	组氨酸	CAU	421	1.45
异亮氨酸	AUU	952	1.52		CCA	263	1.21		CAC	127	0.44
	AUC	391	0.56		CCG	142	0.62	谷氨酰胺	CAA	624	1.59
	AUA	621	0.93	苏氨酸	ACU	431	1.49		CAG	195	0.41
蛋氨酸	AUG	539	1.00		ACC	222	0.84	天冬酰胺	AAU	865	1.45
结页氨酸	GUU	445	1.46		ACA	349	1.21		AAC	281	0.51
	GUC	136	0.37		ACG	131	0.46	赖氨酸	AAA	940	1.57
	GUA	456	1.56	丙氨酸	GCU	526	1.74		AAG	315	0.40
	GUG	177	0.61		GCC	191	0.64	天冬氨酸	GAU	767	1.53
甘氨酸	GGU	485	1.32		GCA	325	1.17		GAC	181	0.47
	GGC	162	0.46		GCG	135	0.45	谷氨酸	GAA	928	1.46
	GGA	577	1.48	精氨酸	CGU	289	1.59		GAG	332	0.54
	GGG	266	0.74		CGC	89	0.47	色氨酸	UGG	381	0.88
半胱氨酸	UGU	194	1.43		CGA	308	1.40
	UGC	61	0.42		CGG	113	0.43

Comparative Analysis of Chloroplast Genomes from Rubuspoliophyllus and Rubus yunanicus

毛叶悬钩子和云南悬钩子叶绿体基因组比较分析

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