朱砂根叶绿体全基因组解析及系统发育分析

doi:10.13560/j.cnki.biotech.bull.1985.2022-0471

摘要/Abstract

摘要：

基于Illumina平台对朱砂根和红凉伞叶绿体全基因组进行测序，利用生物信息学比较叶绿体基因组结构特征与变异程度，旨在明确朱砂根（Ardisia crenata）及红凉伞（Ardisia crenata var. bicolor）叶绿体基因组特征及差异，并与同科其他物种叶绿体全基因组进行比较分析，确定其在紫金牛属系统发育位置。结果表明，朱砂根和红凉伞均为由一个大单拷贝区（LSC）、一个小单拷贝区（SSC）和一对反向重复区（IRa/IRb）构成的环状四分体结构，注释得到132个基因，其重复序列的类型与分布模式相似，但数量有所差异。其中psbA、matK、rpoC2、ropB、ndhK、accD、ndhF、ndhD、ndhH及ycf1等基因的编码区存在差异，这些位点为朱砂根分子鉴定提供新位点。朱砂根及红凉伞叶绿体基因组具有较高保守性，叶绿体基因组之间没有重排或倒置，IR区序列变异最低，SSC区变异程度最高。系统发育树分析表明紫金牛科和报春花科为两个分支，朱砂根和红凉伞归为紫金牛科，且朱砂根与红凉伞亲缘关系最为密切，从分子水平为红凉伞作为朱砂根变种提供了科学解释。本研究解析了朱砂根及变种红凉伞叶绿体基因组结构，探讨了紫金牛科属间系统发育关系，也为紫金牛科药用植物分类鉴定、系统进化及资源开发利用研究奠定基础。

关键词: 紫金牛科, 朱砂根, 红凉伞, 叶绿体基因组, 系统发育

Abstract:

Illumina sequencing platform was used to obtain the whole chloroplast genome sequences of Ardisia crenata. Compared with the structural characteristics and variation degree of chloroplast genomes based on bioinformatics methods, this study is aimed to clarify the characteristics and differences of the chloroplast genomes of A. crenata and Ardisia crenata var. bicolor, to compare and analyze the chloroplast genomes, and to provide reference for the phylogenetic study of Myrsinaceae. As results, both of them were composed of one large single copy region（LSC）, one small single copy region（SSC）and a pair of reverse repeat regions（IRa/IRb）. Total 132 genes were annotated, and their repeat sequence types and distribution patterns were similar, but the number was different. The results of comparative genomics showed that the coding regions of psbA, matK, rpoC2, ropB, ndhK, accD, ndhF, ndhD, ndhH and ycf1 genes were different, and they provided new loci for molecular identification of Ardisia. The chloroplast genome of A. crenata and A. crenata var. bicolor was highly conserved, and there was no rearrangement or inversion between chloroplast genomes. The variation of IR region sequence was the lowest, and the variation degree of SSC region was the highest. In the phylogenetic tree, the A. crenata and A. crenata var. bicolor were sister groups, which clearly reflected the genetic relationship, and provided a scientific explanation for the variety of A. crenata from molecular level. The Myrsinaceae and Primulaceae can be divided into two branches according based on the support rate. In this study, the chloroplast genome structure of A. crenata was analyzed, and the phylogenetic relationship among the genera of Myrsinaceae was discussed, which lays a foundation for the study of taxonomic identification, phylogenetic evolution and resource exploitation and utilization of medicinal plants of Myrsinaceae.

Key words: Myrsinaceae, Ardisia crenata, Ardisia crenata var. bicolor, chloroplast genome, phylogeny

刘雄伟, 刘畅, 曾宪法, 杨小英, 俸婷婷, 赵杰宏, 周英. 朱砂根叶绿体全基因组解析及系统发育分析[J]. 生物技术通报, 2023, 39(1): 232-242.

LIU Xiong-wei, LIU Chang, ZENG Xian-fa, YANG Xiao-ying, FENG Ting-ting, ZHAO Jie-hong, ZHOU Ying. Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes in Ardisia crenata[J]. Biotechnology Bulletin, 2023, 39(1): 232-242.

图/表 10

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物种Species	科属Family & Genus	GenBank 登记号GenBank accession number
百两金Ardisia crispa	紫金牛科Myrsinaceae紫金牛属Ardisia	MW829277.1
走马胎Ardisia gigantifolia	紫金牛科Myrsinaceae紫金牛属Ardisia	MN548760.1
虎舌红Ardisia mamillata	紫金牛科Myrsinaceae紫金牛属Ardisia	MN136062.1
纽子果Ardisia polysticta	紫金牛科Myrsinaceae紫金牛属Ardisia	KC465962.1
酸苔菜Ardisia solanacea	紫金牛科Myrsinaceae紫金牛属Ardisia	MN094783.1
朱砂根Ardisia crenata	紫金牛科Myrsinaceae紫金牛属Ardisia	MW929178.1
紫金牛Ardisia japonica	紫金牛科Myrsinaceae紫金牛属Ardisia	MW166215.1
罗伞树Ardisia quinquegona	紫金牛科Myrsinaceae紫金牛属Ardisia	OK514745.1
白花紫金牛Ardisia merrillii	紫金牛科Myrsinaceae紫金牛属Ardisia	OK054493.1
五花紫金牛Ardisia argenticaulis	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509165.1
花脉紫金牛Ardisia perreticulata	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509164.1
月月红Ardisia faberi	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509169.1
心叶紫金牛Ardisia maclurei	紫金牛科Myrsinaceae紫金牛属Ardisia	MW829278.1
雪下红Ardisia villosa	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509170.1
蜡烛果 Aegiceras corniculatum	紫金牛科Myrsinaceae蜡烛果属Aegiceras	MN167882.1
瘤皮孔酸藤子Embelia scandens	紫金牛科Myrsinaceae酸藤子属Embelia	NC_056316.1
密齿酸藤子Embelia vestita	紫金牛科Myrsinaceae酸藤子属Embelia	MN167884.1
Myrsine sandwicensis	紫金牛科Myrsinaceae铁仔属Myrsine	MN177700.1
光叶铁仔Myrsine stolonifera	紫金牛科Myrsinaceae铁仔属Myrsine	MN167883.1
铁仔Myrsine africana	紫金牛科Myrsinaceae铁仔属Myrsine	MN165129.1
钟花报春 Primula sikkimensis	报春花科Primulaceae报春花属Primula	KX668174.1
鄂报春Primula obconica	报春花科Primulaceae报春花属Primula	KX618681.1
腾冲灯台报春Primula chrysochlora	报春花科Primulaceae报春花属Primula	KX668178.1

物种Species	科属Family & Genus	GenBank 登记号GenBank accession number
百两金Ardisia crispa	紫金牛科Myrsinaceae紫金牛属Ardisia	MW829277.1
走马胎Ardisia gigantifolia	紫金牛科Myrsinaceae紫金牛属Ardisia	MN548760.1
虎舌红Ardisia mamillata	紫金牛科Myrsinaceae紫金牛属Ardisia	MN136062.1
纽子果Ardisia polysticta	紫金牛科Myrsinaceae紫金牛属Ardisia	KC465962.1
酸苔菜Ardisia solanacea	紫金牛科Myrsinaceae紫金牛属Ardisia	MN094783.1
朱砂根Ardisia crenata	紫金牛科Myrsinaceae紫金牛属Ardisia	MW929178.1
紫金牛Ardisia japonica	紫金牛科Myrsinaceae紫金牛属Ardisia	MW166215.1
罗伞树Ardisia quinquegona	紫金牛科Myrsinaceae紫金牛属Ardisia	OK514745.1
白花紫金牛Ardisia merrillii	紫金牛科Myrsinaceae紫金牛属Ardisia	OK054493.1
五花紫金牛Ardisia argenticaulis	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509165.1
花脉紫金牛Ardisia perreticulata	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509164.1
月月红Ardisia faberi	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509169.1
心叶紫金牛Ardisia maclurei	紫金牛科Myrsinaceae紫金牛属Ardisia	MW829278.1
雪下红Ardisia villosa	紫金牛科Myrsinaceae紫金牛属Ardisia	OK509170.1
蜡烛果 Aegiceras corniculatum	紫金牛科Myrsinaceae蜡烛果属Aegiceras	MN167882.1
瘤皮孔酸藤子Embelia scandens	紫金牛科Myrsinaceae酸藤子属Embelia	NC_056316.1
密齿酸藤子Embelia vestita	紫金牛科Myrsinaceae酸藤子属Embelia	MN167884.1
Myrsine sandwicensis	紫金牛科Myrsinaceae铁仔属Myrsine	MN177700.1
光叶铁仔Myrsine stolonifera	紫金牛科Myrsinaceae铁仔属Myrsine	MN167883.1
铁仔Myrsine africana	紫金牛科Myrsinaceae铁仔属Myrsine	MN165129.1
钟花报春 Primula sikkimensis	报春花科Primulaceae报春花属Primula	KX668174.1
鄂报春Primula obconica	报春花科Primulaceae报春花属Primula	KX618681.1
腾冲灯台报春Primula chrysochlora	报春花科Primulaceae报春花属Primula	KX668178.1

类别 Type	长度Length/bp			GC含量GC content/%
类别 Type	朱砂根（贵州） A. crenata (Guizhou)	朱砂根（江西） A. crenata (Jiangxi)	红凉伞 A.crenata var. bicolor	朱砂根（贵州） A.crenata (Guizhou)	朱砂根（江西） A. crenata (Jiangxi)	红凉伞 A.crenata var. bicolor
总长 Tota length/bp	156 538	156 540	156 535	37.09	37.09	37.09
大单拷贝区LSC/bp	86 107	86 110	86 104	34.97	34.97	34.97
反向重复区Ira/bp	26 050	26 050	26 050	43.02	43.01	43.01
小单拷贝区SSC/bp	18 331	18 330	18 331	30.18	30.2	30.17
反向重复区IRb/bp	26 050	26 050	26 050	43.02	43.01	43.01

类别 Type	长度Length/bp			GC含量GC content/%
类别 Type	朱砂根（贵州） A. crenata (Guizhou)	朱砂根（江西） A. crenata (Jiangxi)	红凉伞 A.crenata var. bicolor	朱砂根（贵州） A.crenata (Guizhou)	朱砂根（江西） A. crenata (Jiangxi)	红凉伞 A.crenata var. bicolor
总长 Tota length/bp	156 538	156 540	156 535	37.09	37.09	37.09
大单拷贝区LSC/bp	86 107	86 110	86 104	34.97	34.97	34.97
反向重复区Ira/bp	26 050	26 050	26 050	43.02	43.01	43.01
小单拷贝区SSC/bp	18 331	18 330	18 331	30.18	30.2	30.17
反向重复区IRb/bp	26 050	26 050	26 050	43.02	43.01	43.01

基因类别 Gene category	基因功能 Gene function	基因名称 Gene name
光合作用基因 Photosynthesis gene	ATP 合酶亚基Subunits of ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	亚光系统 I Subunits of photosystem I	psaA、psaB、psaC、psaI、psaJ
	亚光系统 II Subunits of photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ、ycf3
	NADH-脱氢酶亚基Subunits of NADH-dehydrogenase	ndhA、ndhB（×2）、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	细胞色素复合物 b/f 亚基 Subunits of cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	Rubisco 酶亚基	rbcL
复制基因Replicator	核糖体 RNA 基因 Ribosome RNA genes	rrn16S（×2）、rrn23S（×2）、rrn5S（×2）、rrn4.5S（×2）、
	转运 RNA 基因Transfer RNA genes	tRNA-Ala（×2）、tRNA-Arg（×3）、tRNA-Asn（×2）、tRNA-Asp、tRNA-Cys（×2）、tRNA-Gln、tRNA-Glu、tRNA-Gly（×2）、tRNA-His、tRNA-Ile（×2）、tRNA-Leu（×4）、tRNA-Lys、tRNA-Met（×4）、tRNA-Phe、tRNA-Pro、tRNA-Ser（×3）、tRNA-Thr、tRNA-Trp、tRNA-Tyr、tRNA-Val（×2）
	核糖体大亚基Large subunit of ribosome	rpl14、rpl16、rpl2（×2）、rpl20、rpl22、rpl23（×2）、rpl32、rpl33、rpl36
	核糖体小亚基Small subunit of ribosome	rps11、rps12（×2）、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7（×2）、rps8
	DNA 依赖核酸聚合酶DNA-dependent RNA polymerase	rpoA、rpoB、rpoC1、rpoC2
其他基因 Other genes	乙酰辅酶 A 羧化酶亚基Subunit of acetyl-CoA-carboxylase	accD
	c 型细胞色素合成基因c-Type cytochrome synthesis gene	ccsA
	包裹膜蛋白Envelop membrane protein	cemA
	蛋白酶Protease	clpP
	转录起始因子Translational initiation factor	infA
	成熟酶Maturase	matK
未知基因Unknown gene	保守开放性阅读框Conservative open reading box	ycf1、ycf2（×2）、ycf4、yfc15（×2）