连翘叶绿体基因组特征分析

doi:10.16420/j.issn.0513-353x.2020-0781

摘要/Abstract

摘要：

为探究连翘叶绿体基因组特征及该属物种的系统进化发育关系,利用高通量测序技术对连翘长花柱与短花柱植株叶绿体基因组进行测序和功能注释,利用PCR对高通量测序结果进行验证。结果显示：连翘长花柱与短花柱植株叶绿体基因组全长均为156 386 bp,为典型的四段式结构。连翘叶绿体基因组注释到114个基因,包括80个蛋白编码基因,30个tRNA基因,4个rRNA基因。基因组56个简单重复序列（SSR）位点分析显示其SSR序列主要由A和T碱基组成。连翘叶绿体基因组编码区偏向使用A、T碱基,但整体密码子偏好性较弱,主要表现在Arg和Ser的差异。与已公布的32种植物（包括14种连翘属）叶绿体基因组序列构建系统发育进化树,结果显示连翘的叶绿体基因组与产自山西泽州的连翘高度同源。连翘异型花柱具有相同的叶绿体基因组序列,推测连翘的异型花柱是由同型花演化而来。

关键词: 连翘, 异型花柱, 叶绿体基因组, SSR, 密码子偏好性, 系统发育分析

Abstract:

In order to explore the chloroplasts genomic characteristics of Forsythia suspensa and the phylogenetic development of this genus,high-throughput sequencing technology was used to sequence and functionally annotate the chloroplast genomes of long and short style type in F. suspensa. PCR was used to confirm the sequencing results. The results showed that the chloroplast genomes of the long and short styles type were 156 386 bp,which was a typical four-segment structure in F. suspensa. A total of 114 unique genes were annotated,including 80 protein-coding genes,30 tRNA,and four rRNA. Analysis of 56 simple sequence repeats（SSRs）showed that it mainly composes of A and T bases. In addition,the coding region of the chloroplast genome of F. suspensa prefers to use A and T bases,but the overall codon preference is weak,which is mainly reflected by the difference of Arg and Ser. Based on the chloroplast genome sequence of the heterostyly and 32 plants’ chloroplast genome sequences（including 14 species of Forsythia）published the phylogenetic relationship is analyzed. And the results showed that the chloroplast genome of heterostyly was highly homologous to F. suspensa in Zezhou,Shanxi. It is possible that heterostyly also evolved from the homostyly flowers in F. suspensa.

Key words: Forsythia suspensa, heterostyly, chloroplast genome, SSR, codon preference, phylogenetic analysis

中图分类号:

S685.24

宋芸, 贾孟君, 曹亚萍, 李政, 贺嘉欣, 王勇飞, 张鑫瑞, 乔永刚. 连翘叶绿体基因组特征分析[J]. 园艺学报, 2022, 49(1): 187-199.

SONG Yun, JIA Mengjun, CAO Yaping, LI Zheng, HE Jiaxin, WANG Yongfei, ZHANG Xinrui, QIAO Yonggang. Analysis on Chloroplast Genomic Characteristics of Forsythia suspensa[J]. Acta Horticulturae Sinica, 2022, 49(1): 187-199.

图/表 10

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类型 Type	大小/bp Size				基因数量 Number of genes				GC/%
类型 Type	LSC	SSC	IR	总数 Total	Protein	tRNA	rRNA	总计 Total	LSC	SSC	IR	平均 Mean
长花柱 Long-styled morph	87 142	17 810	25 717	156 386	80	30	4	114	35.8	31.8	43.2	37.8
短花柱 Short style type	87 595	17 781	25 717	156 810	80	30	4	114	35.8	31.9	43.2	37.8

类型 Type	大小/bp Size				基因数量 Number of genes				GC/%
类型 Type	LSC	SSC	IR	总数 Total	Protein	tRNA	rRNA	总计 Total	LSC	SSC	IR	平均 Mean
长花柱 Long-styled morph	87 142	17 810	25 717	156 386	80	30	4	114	35.8	31.8	43.2	37.8
短花柱 Short style type	87 595	17 781	25 717	156 810	80	30	4	114	35.8	31.9	43.2	37.8

功能 Function	基因家族 Family Name	基因ID Gene ID
光合作用相关基因（45） Photosynthesis related genes	核酮糖-1,5-二磷酸羧化酶 Rubisco	rbcL
	ATP合酶 ATP Synthase	atpA,atpB,atpE,atpF,atpH,atpI*
	NADH脱氢酶 NADH Dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素 Cytochrome	petA,petB,petD,petG,petL,petN,ccsA
	光合系统Ⅰ PhotosystemⅠ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ PhotosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
转录翻译相关基因（60） Transcription and translation related genes	大亚基核糖体 Large Subunit of Ribosome	rpl2,rpl14,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	小亚基核糖体Small Subunit of Ribosome	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	DNA依赖性RNA聚合酶 DNA Dependent RNA Polymerase	rpoA,rpoB,rpoC1,rpoC2*
	核糖体RNA rRNA Genes	rrn5,rrn4.5,rrn16,rrn23
	转运RNA tRNA Genes	trnA-UGC,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
	翻译起始因子 Translation Initiation Factor	infA
其他基因（4） Other genes	乙酰辅酶A羧化酶 Acety1-CoA carboxylase	accD
	包膜蛋白 Envelop membrane protein	cemA
	成熟酶 Maturase	matK
	clpP样蛋白酶 clpP-like protease	clpP*
功能未知基因（5） Unknown	保守开放阅读框Conserved open reading frames	ycf1,ycf2,ycf3,ycf4,ycf15*

功能 Function	基因家族 Family Name	基因ID Gene ID
光合作用相关基因（45） Photosynthesis related genes	核酮糖-1,5-二磷酸羧化酶 Rubisco	rbcL
	ATP合酶 ATP Synthase	atpA,atpB,atpE,atpF,atpH,atpI*
	NADH脱氢酶 NADH Dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素 Cytochrome	petA,petB,petD,petG,petL,petN,ccsA
	光合系统Ⅰ PhotosystemⅠ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ PhotosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
转录翻译相关基因（60） Transcription and translation related genes	大亚基核糖体 Large Subunit of Ribosome	rpl2,rpl14,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	小亚基核糖体Small Subunit of Ribosome	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	DNA依赖性RNA聚合酶 DNA Dependent RNA Polymerase	rpoA,rpoB,rpoC1,rpoC2*
	核糖体RNA rRNA Genes	rrn5,rrn4.5,rrn16,rrn23
	转运RNA tRNA Genes	trnA-UGC,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
	翻译起始因子 Translation Initiation Factor	infA
其他基因（4） Other genes	乙酰辅酶A羧化酶 Acety1-CoA carboxylase	accD
	包膜蛋白 Envelop membrane protein	cemA
	成熟酶 Maturase	matK
	clpP样蛋白酶 clpP-like protease	clpP*
功能未知基因（5） Unknown	保守开放阅读框Conserved open reading frames	ycf1,ycf2,ycf3,ycf4,ycf15*

差异 Difference	长花柱/bp Long style type site	短花柱/bp Short style type site
SNP₁	-	4 705（A）
SNP₂	6 923（T）	-
SNP₃	-	6 973（T）
SNP₄	21 955（G）	21 956（A）
SNP₅	21 964（A）	21 964（C）
SNP₆	-	31 777（C）
Gap₁	-	31 805 ~ 32 018
SNP₇	32 238（G）	32 454（T）
SNP₈	32 243（G）	32 459（T）
Gap₂	-	32 624 ~ 32 859
SNP₉	-	60 082（C）
SNP₁₀	115 112（A）	-
Gap₃	115 316 ~ 115 343	-
SNP₁₁	115 705（G）	115 528（C）
SNP₁₂	115 919（A）	116 343（G）