陕甘花楸叶绿体基因组及其与爪瓣花楸的系统关系

doi:10.16420/j.issn.0513-353x.2020-1021

摘要/Abstract

摘要：

采用高通量测序技术分析了陕甘花楸（Sorbus koehneana）的叶绿体全基因组,并探讨其与爪瓣花楸（S. unguiculata）的关系。陕甘花楸叶绿体基因组全长159 873 bp,GC含量为36.60%,呈典型的四分体结构,包含1个小单拷贝区（SSC,19 218 bp）、1个大单拷贝区（LSC,87 899 bp）和1对反向重复序列（IRa和IRb,26 378 bp）;共注释到108个基因,包括76个蛋白编码基因,4个rRNA基因,28个tRNA基因;检测到47个简单重复序列（SSR）和48个分散重复序列（INE）。花楸属植物叶绿体基因组在大小、基因类型、密码子、内含子和GC含量等方面高度保守,但不同的重复序列和位于非编码区的12个变异热点区域可用作后续物种遗传多样性和亲缘关系研究。系统发育分析结果显示陕甘花楸位于花楸属复叶亚属,与爪瓣花楸和钝齿花楸（S. helenae）亲缘关系较近;不支持将爪瓣花楸作为陕甘花楸的异名处理,建议恢复爪瓣花楸物种名称。

关键词: 花楸, 叶绿体基因组, 基因组比较, 系统演化分析

Abstract:

The complete chloroplast（cp）genome of Sorbus koehneana and its phylogenetic relationship with S. unguiculata were analyzed. The complete cp genome of S. koehneana is 159 873 bp in size with 36.60% GC content. It has a typical quadripartite structure including a small single copy（SSC）region of 19 218 bp,a large single copy（LSC）region of 87 899 bp and a pair of inverted repeat regions （IRs）of 26 378 bp. The cp genome encodes 108 genes,comprising 76 protein-coding genes,four rRNA genes and 28 tRNA genes. Additionally,47 simple sequence repeats（SSRs）and 48 interspersed nuclear elements（INEs）were identified. In Sorbus,cp genome is highly conserved in length,gene type,codon number,intron number and GC content. However,the different sequence repeats and 12 highly variable regions located in intergenic spacers may be used for population genetic and phylogenetic studies in future. Phylogenetic analyses revealed that S. koehneana,S. unguiculata and S. helenae are in the same lineage nested within Sorbus subg. Sorbus. However,S. unguiculata is sister to S. helenae instead of S. koehneana. So the treatment of S. unguiculata as a synonym of S. koehneana is not supported and the name S. unguiculata is proposed to be reinstated here.

Key words: Sorbus, chloroplast genome, genomic comparison, phylogenetic analysis

中图分类号:

S685.99

汤晨茜, 仇志欣, 檀超, 钱羽铭, 陈昕. 陕甘花楸叶绿体基因组及其与爪瓣花楸的系统关系[J]. 园艺学报, 2022, 49(3): 641-654.

TANG Chenqian, QIU Zhixin, TAN Chao, QIAN Yuming, CHEN Xin. Sorbus koehneana（Rosaceae）：Its Complete Chloroplast Genome and Phylogenetic Relationship with S. unguiculata[J]. Acta Horticulturae Sinica, 2022, 49(3): 641-654.

图/表 8

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基因功能 Function of gene	基因分类 Group of genes	基因代码 Code	基因 Gene
自我复制 Self replication	rRNA	rrn	rrn4.5^c,rrn5^c,rrn16^c,rrn23^c
	tRNA	trn	trnA-UGC^ac,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-UCC,trnH-GUG,trnI-CAU^c,trnI-GAU^ac,trnK-UUU^a,trnL-CAA^c,trnL-UAA^a,trnL-UAG,trnM-CAU,trnN-GUU^c,trnP-UGG,trnQ-UUG,trnR-ACG^c,trnR-UCU,trnS-GCU,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC^c,trnV-UAC^a,trnW-CCA,trnY-GUA
	核糖体小亚基 Ribosomal proteins（SSU）	rps	rps2,rps3,rps4,rps7^c,rps8,rps11,rps12^acd,rps14,rps15,rps16^a,rps18,rps19
	核糖体大亚基 Ribosomal proteins（LSU）	rpl	rpl2^ac,rpl14,rpl16^a,rpl20,rpl22,rpl23^ac,rpl32,rpl33,rpl336
	RNA 聚合酶亚基RNA polymerase	rpo	rpoA,rpoB,rpoC1^a,rpoC2
光合作用 Genes for photosynthesis	光合系统Ⅰ Photosystem Ⅰ	psa	psaA,psaB,psaJ,psaI
	光合系统Ⅱ Photosystem Ⅱ	psb	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbM,psbN,psbT,psbZ
	细胞色素复合物Cytochrome b/f complex	pet	petA,petB^a,petD^a,petG,petL,petN
	ATP合成酶ATP synthase	atp	atpA,atpB,atpE,atpF^a,atpH,atpI
	NADH脱氢酶 Subunits of NADH-dehydrogenase	ndh	ndhA^a,ndhB^ac,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	二磷酸核酮糖羧化酶大亚基 Subunit of rubisco	rbc	rbcL
其他基因 Other genes	乙酰CoA羧化酶 Subunit of Acetyl-CoA-carboxylase	acc	accD
	膜包被蛋白基因 Envelop membrane protein gene	cem	cemA
	c型细胞色素合成基因 c-type cytochrom synthesis gene	ccs	ccsA
	蛋白酶基因Protease gene	clp	clpP^b
	成熟酶基因Maturase gene	mat	matK
未知功能 Unknow function	假想叶绿体读码框 Hypothetical chloroplast reading frames	ycf	ycf1,ycf2^c,ycf3^b,ycf4

基因功能 Function of gene	基因分类 Group of genes	基因代码 Code	基因 Gene
自我复制 Self replication	rRNA	rrn	rrn4.5^c,rrn5^c,rrn16^c,rrn23^c
	tRNA	trn	trnA-UGC^ac,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-UCC,trnH-GUG,trnI-CAU^c,trnI-GAU^ac,trnK-UUU^a,trnL-CAA^c,trnL-UAA^a,trnL-UAG,trnM-CAU,trnN-GUU^c,trnP-UGG,trnQ-UUG,trnR-ACG^c,trnR-UCU,trnS-GCU,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC^c,trnV-UAC^a,trnW-CCA,trnY-GUA
	核糖体小亚基 Ribosomal proteins（SSU）	rps	rps2,rps3,rps4,rps7^c,rps8,rps11,rps12^acd,rps14,rps15,rps16^a,rps18,rps19
	核糖体大亚基 Ribosomal proteins（LSU）	rpl	rpl2^ac,rpl14,rpl16^a,rpl20,rpl22,rpl23^ac,rpl32,rpl33,rpl336
	RNA 聚合酶亚基RNA polymerase	rpo	rpoA,rpoB,rpoC1^a,rpoC2
光合作用 Genes for photosynthesis	光合系统Ⅰ Photosystem Ⅰ	psa	psaA,psaB,psaJ,psaI
	光合系统Ⅱ Photosystem Ⅱ	psb	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbM,psbN,psbT,psbZ
	细胞色素复合物Cytochrome b/f complex	pet	petA,petB^a,petD^a,petG,petL,petN
	ATP合成酶ATP synthase	atp	atpA,atpB,atpE,atpF^a,atpH,atpI
	NADH脱氢酶 Subunits of NADH-dehydrogenase	ndh	ndhA^a,ndhB^ac,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	二磷酸核酮糖羧化酶大亚基 Subunit of rubisco	rbc	rbcL
其他基因 Other genes	乙酰CoA羧化酶 Subunit of Acetyl-CoA-carboxylase	acc	accD
	膜包被蛋白基因 Envelop membrane protein gene	cem	cemA
	c型细胞色素合成基因 c-type cytochrom synthesis gene	ccs	ccsA
	蛋白酶基因Protease gene	clp	clpP^b
	成熟酶基因Maturase gene	mat	matK
未知功能 Unknow function	假想叶绿体读码框 Hypothetical chloroplast reading frames	ycf	ycf1,ycf2^c,ycf3^b,ycf4

基因 Gene	位置 Location	内含子 I/bp Intron I	内含子II/bp Intron II	外显子 I/bp Exon I	外显子II/bp Exon II	外显子 III/bp Exon III
atpF	LSC	729		144	411
petB	LSC	797		5	643
petD	LSC	724		7	476
rpl16	LSC	977		10	398
rpoC1	LSC	741		435	1 611
rps16	LSC	867		40	230
trnL-UAA	LSC	514		37	50
trnV-UAC	LSC	592		39	37
ndhA	SSC	1 120		552	540
ndhB	IR	669		777	756
rpl2	IR	686		389	436
rps12	IR	541		231	30
clpP	LSC	823	638	71	289	228
ycf3	LSC	698	745	126	228

基因 Gene	位置 Location	内含子 I/bp Intron I	内含子II/bp Intron II	外显子 I/bp Exon I	外显子II/bp Exon II	外显子 III/bp Exon III
atpF	LSC	729		144	411
petB	LSC	797		5	643
petD	LSC	724		7	476
rpl16	LSC	977		10	398
rpoC1	LSC	741		435	1 611
rps16	LSC	867		40	230
trnL-UAA	LSC	514		37	50
trnV-UAC	LSC	592		39	37
ndhA	SSC	1 120		552	540
ndhB	IR	669		777	756
rpl2	IR	686		389	436
rps12	IR	541		231	30
clpP	LSC	823	638	71	289	228
ycf3	LSC	698	745	126	228

氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number	氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number	氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number
苯丙氨酸Phe	UUU	1.29	932	脯氨酸Pro	CCU	1.50	375	谷氨酸Glu	GAA	1.46	957
	UUC	0.71	516		CCC	0.75	186		GAG	0.54	350
亮氨酸Leu	UUA	1.92	857		CCA	1.18	294	半胱氨酸Cys	UGU	1.44	245
	UUG	1.20	537		CCG	0.57	143		UGC	0.56	95
	CUU	1.28	571	苏氨酸Thr	ACU	1.57	509	色氨酸Trp	UGG	1.00	457
	CUC	0.41	182		ACC	0.71	232	精氨酸Arg	CGU	1.20	317
	CUA	0.79	351		ACA	1.24	402		CGC	0.41	107
	CUG	0.40	179		ACG	0.48	156		CGA	1.37	361
异亮氨酸Ile	AUU	1.47	1 082	丙氨酸Ala	GCU	1.82	591		CGG	0.49	128
	AUC	0.59	435		GCC	0.65	212		AGA	1.83	482
	AUA	0.94	696		GCA	1.10	358		AGG	0.70	184
甲硫氨酸Met	AUG	1.00	591		GCG	0.43	140	络氨酸Tyr	UAU	1.57	780
缬氨酸Val	GUU	1.47	493	组氨酸His	CAU	1.52	466		UAC	0.43	214
	GUC	0.44	149		CAC	0.48	146	甘氨酸Gly	GGU	1.29	551
	GUA	1.52	511	谷氨酰胺Gln	CAG	1.52	698		GGC	0.41	177
	GUG	0.56	189		CAA	0.48	218		GGA	1.61	687
丝氨酸Ser	UCU	1.64	561	天冬酰胺Asn	AAU	1.51	961		GGG	0.69	293
	UCC	0.99	338		AAC	0.49	313	终止子	UAA	1.17	65
	UCA	1.19	407	赖氨酸Lys	AAA	1.47	1 027	Terminator	UAG	0.86	48
	UCG	0.61	209		AAG	0.53	373		UGA	0.97	54
	AGU	1.14	389	天冬氨酸Asp	GAU	1.61	846
	AGC	0.44	151		GAC	0.39	202
总计Total			25 726