球花石斛（Dendrobium thyrsiflorum）叶绿体基因组特征及亲缘关系解析

doi:10.13560/j.cnki.biotech.bull.1985.2020-1380

摘要/Abstract

摘要：

球花石斛（Dendrobium thyrsiflorum）主要分布在我国云南地区,是非常重要的传统中药材及观赏花卉。本研究整合二代、三代测序数据,从头组装了球花石斛的完整叶绿体基因组。球花石斛叶绿体基因组全长151 686 bp,为典型的四分结构,包含106个unigenes,其中编码基因71个,tRNA 31个,rRNA 4个。球花石斛叶绿体基因组检测到58个SSR（simple sequence repeat）位点,以单碱基重复A/T类型为主。密码子偏好性分析显示,亮氨酸为使用频率最高的氨基酸（10.15%）,具有偏好性的密码子有31个,且绝大多数偏好性密码子以A/U结尾。通过共有编码基因序列（coding sequence,CDs）对27种石斛进行系统进化分析,将所选石斛分为9大类群,其中球花石斛与霍山石斛亲缘关系密切。本研究结果阐明了球花石斛的叶绿体基因组特征,为其资源筛选、鉴定,遗传多样性分析提供分子依据。

关键词: 球花石斛, 叶绿体基因组, 高通量测序, 系谱分析

Abstract:

Dendrobium thyrsiflorum,which is widely distributed in Yunnan province,is an important garden flower and used as a traditional Chinese medicine. In the present study,we de novo assembled the complete chloroplast（CP）genome of D. thyrsiflorum through the integration of the PacBio long and Illumina short reads. The CP genome exhibited a typical quadripartite cycle of 151 686 bp containing 106 unigenes,and they were 71 encoding genes,31 tRNA genes and 4 rRNA genes. Additionally,58 SSR（simple sequence repeat）loci dominantly occupied by the type of A/T were detected in the CP genome. Codon bias analysis showed that the leucine was preferentially used at 10.15% frequency,there were 31 biased codons and the majority of the biased codons were ended with A/U. Phylogenetic analysis using 27 CP genomes of the Dendrobium based on the common coding sequence,we classified these Dendrobium species into 9 groups,and D. thyrsiflorum presented the closest relationship with D. huoshanense. This study comprehensively deciphered the characteristics of D. thyrsiflorum genome,which may provide molecular information for future resources selection and identification,and genetic diversity analysis.

Key words: Dendrobium thyrsiflorum, chloroplast genome, high-throughput sequencing, phylogenetic analysis

朱斌, 甘晨晨, 王洪程. 球花石斛（Dendrobium thyrsiflorum）叶绿体基因组特征及亲缘关系解析[J]. 生物技术通报, 2021, 37(5): 38-47.

ZHU Bin, GAN Chen-chen, WANG Hong-cheng. Characteristics of the Complete Chloroplast Genome of Dendrobium thyrsiflorum and Its Phylogenetic Relationship Analysis[J]. Biotechnology Bulletin, 2021, 37(5): 38-47.

图/表 8

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范畴 Category	条目 Item	描述 Description
叶绿体基因组结构 Structure of cp genome	长编码区/bp	84 749
	反向重复区/bp	26 293
	短编码区/bp	14 351
	基因组大小/bp	151 686
基因组成 Gene content	基因总数	106
	编码基因	71
	tRNAs	31
	rRNAs	4
	两拷贝基因	19
	长编码区基因数	78
	反向重复区基因数	18
	短编码区基因数	8
	基因总长度/bp	71 241
	基因平均长度/bp	913
	基因/基因组/%	46.97
GC含量 GC content	长编码区GC含量/%	35.1
	反向重复区GC含量/%	43.43
	短编码区GC含量/%	30.44
	平均GC含量/%	37.55

范畴 Category	条目 Item	描述 Description
叶绿体基因组结构 Structure of cp genome	长编码区/bp	84 749
	反向重复区/bp	26 293
	短编码区/bp	14 351
	基因组大小/bp	151 686
基因组成 Gene content	基因总数	106
	编码基因	71
	tRNAs	31
	rRNAs	4
	两拷贝基因	19
	长编码区基因数	78
	反向重复区基因数	18
	短编码区基因数	8
	基因总长度/bp	71 241
	基因平均长度/bp	913
	基因/基因组/%	46.97
GC含量 GC content	长编码区GC含量/%	35.1
	反向重复区GC含量/%	43.43
	短编码区GC含量/%	30.44
	平均GC含量/%	37.55

基因范畴 Gene categories	基因功能 Gene group	基因名 Gene names
参与光合作用的基因 Genes involving in photosynthesis	光合系统亚基	ndhJ,pbf1,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbT,psbZ
	细胞色素复合体亚基	petA,petB^b,petD^b,petG,petL,petN
	二磷酸核酮糖羧化酶大亚基	rbcL
	ATP合成酶亚基	atpA,atpB,atpE,atpF^b,atpH,atpI
	NADH脱氢酶亚基	ndhA,ndhB^a,b
自体复制相关基因 Self-replication	rRNA基因	rrn16^a,rrn23^a,rrn4.5^a,rrn5^a
	tRNA基因	trnA-UGC^a,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^b,trnG-UCC,trnH-GUG^a,trnI-CAU^a,trnI-GAU^a,b,trnK-UUU^b,trnL-CAA^a,trnL-UAA^b,trnL-UAG,trnM-CAU,trnN-GUU^a,trnP-UGG,trnQ-UUG,trnR-ACG^a,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-CGU,trnT-GGU,trnT-UGU,trnV-GAC^a,trnV-UAC^a,b,trnW-CCA,trnY-GUA
	核糖体小亚基	rps11,rps12^a,c,rps14,rps15,rps16^b,rps18,rps19^a,rps2
	核糖体大亚基	rps3,rps4,rps7^a,rps8,rpl14,rpl16^b,rpl2^a,b,rpl20,rpl22,rpl23^a,rpl32,rpl33
	DNA依赖的RNA聚合酶	rpl36,rpoA,rpoB,rpoC1^b,rpoC2
其它功能基因 Other genes	成熟酶	matK
	翻译起始因子	infA
	蛋白质膜基因	cemA
	乙酰辅酶A亚基	accD
	C类型细胞色素合成基因	ccsA
	蛋白酶	clpP^c
未知功能基因 Nonfunctional genes	保守的开放阅读框	ycf1,ycf2^a,ycf3^c,ycf4

基因范畴 Gene categories	基因功能 Gene group	基因名 Gene names
参与光合作用的基因 Genes involving in photosynthesis	光合系统亚基	ndhJ,pbf1,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbT,psbZ
	细胞色素复合体亚基	petA,petB^b,petD^b,petG,petL,petN
	二磷酸核酮糖羧化酶大亚基	rbcL
	ATP合成酶亚基	atpA,atpB,atpE,atpF^b,atpH,atpI
	NADH脱氢酶亚基	ndhA,ndhB^a,b
自体复制相关基因 Self-replication	rRNA基因	rrn16^a,rrn23^a,rrn4.5^a,rrn5^a
	tRNA基因	trnA-UGC^a,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^b,trnG-UCC,trnH-GUG^a,trnI-CAU^a,trnI-GAU^a,b,trnK-UUU^b,trnL-CAA^a,trnL-UAA^b,trnL-UAG,trnM-CAU,trnN-GUU^a,trnP-UGG,trnQ-UUG,trnR-ACG^a,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-CGU,trnT-GGU,trnT-UGU,trnV-GAC^a,trnV-UAC^a,b,trnW-CCA,trnY-GUA
	核糖体小亚基	rps11,rps12^a,c,rps14,rps15,rps16^b,rps18,rps19^a,rps2
	核糖体大亚基	rps3,rps4,rps7^a,rps8,rpl14,rpl16^b,rpl2^a,b,rpl20,rpl22,rpl23^a,rpl32,rpl33
	DNA依赖的RNA聚合酶	rpl36,rpoA,rpoB,rpoC1^b,rpoC2
其它功能基因 Other genes	成熟酶	matK
	翻译起始因子	infA
	蛋白质膜基因	cemA
	乙酰辅酶A亚基	accD
	C类型细胞色素合成基因	ccsA
	蛋白酶	clpP^c
未知功能基因 Nonfunctional genes	保守的开放阅读框	ycf1,ycf2^a,ycf3^c,ycf4

密码子 Codon	数目 Number	氨基酸 Amino acids	密码子比例 Ratio/%	氨基酸数目 Number of amino acids	氨基酸比例 Ratio/%	相对密码子使用度 RSCU
GCA	369	丙氨酸 Ala	1.55	1 235	5.2	1.2
GCC	176		0.74			0.57
GCG	122		0.51			0.4
GCU	568		2.39			1.84
AGA	489	精氨酸 Arg	2.06	1 509	6.35	1.94
AGG	160		0.67			0.64
CGA	333		1.4			1.32
CGC	84		0.35			0.33
CGG	102		0.43			0.41
CGU	341		1.44			1.36
AAC	257	天冬酰胺Asn	1.08	1 114	4.69	0.46
AAU	857	天冬酰胺Asn	3.61	1 114	4.69	1.54
GAC	181	天冬氨酸Asp	0.76	998	4.2	0.36
GAU	817	天冬氨酸Asp	3.44	998	4.2	1.64
UGC	72	半胱氨酸Cys	0.3	279	1.17	0.52
UGU	207	半胱氨酸Cys	0.87	279	1.17	1.48
CAA	655	谷氨酰胺Gln	2.76	872	3.67	1.5
CAG	217	谷氨酰胺Gln	0.91	872	3.67	0.5
GAA	964	谷氨酸 Glu	4.06	1 317	5.55	1.46
GAG	353	谷氨酸 Glu	1.49	1 317	5.55	0.54
GGA	636	甘氨酸 Gly	2.68	1 585	6.67	1.61
GGC	152		0.64			0.38
GGG	286		1.2			0.72
GGU	511		2.15			1.29
CAC	130	组氨酸 His	0.55	599	2.52	0.43
CAU	469	组氨酸 His	1.97	599	2.52	1.57
AUA	581	异亮氨酸 Ile	2.44	1 959	8.25	0.89
AUC	434		1.83			0.66
AUU	944		3.98			1.45
CUA	352	亮氨酸 Leu	1.48	2 410	10.15	0.88
CUC	169		0.71			0.42
CUG	172		0.72			0.43
CUU	509		2.14			1.27
UUA	716		3.02			1.78
UUG	492		2.07			1.22
AAA	972	赖氨酸 Lys	4.09	1 353	5.7	1.44
AAG	381	赖氨酸 Lys	1.6	1 353	5.7	0.56
AUG	549	甲硫氨酸Met	2.31	549	2.31	1
UUC	509	苯丙氨酸Phe	2.14	1 328	5.59	0.77
UUU	819	苯丙氨酸Phe	3.45	1 328	5.59	1.23
CCA	268	脯氨酸 Pro	1.13	970	4.08	1.11
CCC	217		0.91			0.89
CCG	112		0.47			0.46
CCU	373		1.57			1.54
AGC	99	丝氨酸 Ser	0.42	1 891	7.96	0.31
AGU	377		1.59			1.2
UCA	366		1.54			1.16
UCC	322		1.36			1.02
UCG	161		0.68			0.51
UCU	566		2.38			1.8
UAA	35	终止密码子TER	0.15	78	0.33	1.35
UAG	26		0.11			1
UGA	17		0.07			0.65
ACA	352	苏氨酸 Thr	1.48	1197	5.04	1.18
ACC	219		0.92			0.73
ACG	148		0.62			0.49
ACU	478		2.01			1.6
UGG	415	色氨酸 Trp	1.75	415	1.75	1
UAC	166	络氨酸 Tyr	0.7	822	3.46	0.4
UAU	656	络氨酸 Tyr	2.76	822	3.46	1.6
GUA	454	缬氨酸 Val	1.91	1267	5.34	1.43
GUC	164		0.69			0.52
GUG	215		0.91			0.68
GUU	434		1.83			1.37