Chloroplast Genome Analysis of <italic style="font-style: italic">Liriope spicata</italic> var. <italic style="font-style: italic">prolifera, Ophiopogon japonicus</italic> in Sichuan and Zhejiang

Meng-han WANG; Shuai-jun HU; Chu-hong YANG; Xia LIU; Jiang XU

doi:10.13422/j.cnki.syfjx.20200947

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Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang

Pharmacy Fundamentals | 更新时间：2021-02-09

- Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang
- Chinese Journal of Experimental Traditional Medical Formulae Vol. 26, Issue 8, Pages: 182-191(2020)
- 作者机构：
  
  1.武汉理工大学　化学化工与生命科学学院，武汉　 430070
  2.中国中医科学院　中药研究所，北京　 100700
- 作者简介：
- 基金信息：
- DOI：10.13422/j.cnki.syfjx.20200947
  CLC： R22; R931; R28; Q34; Q732
- Received：04 December 2019，
  
  Published Online：14 January 2020，
  
  Published：20 April 2020
- 稿件说明：
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Meng-han WANG, Shuai-jun HU, Chu-hong YANG, et al. Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang[J]. Chinese journal of experimental traditional medical formulae, 2020, 26(8): 182-191.
DOI：

Meng-han WANG, Shuai-jun HU, Chu-hong YANG, et al. Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang[J]. Chinese journal of experimental traditional medical formulae, 2020, 26(8): 182-191. DOI： 10.13422/j.cnki.syfjx.20200947.

摘要

目的：

测定湖北麦冬、川麦冬及杭麦冬叶绿体基因组，分析其序列特征并完成特异性DNA条形码筛选。

方法：

通过高通量测序技术对湖北麦冬、川麦冬及杭麦冬叶绿体基因组进行测序、拼接及注释，利用生物信息学方法对叶绿体基因组结构特征及系统发育进行分析。

结果：

湖北麦冬的叶绿体基因组全长155 998 bp，鸟嘌呤与胞嘧啶(GC)总量37.7%，成功注释出85个蛋白编码基因，37个转运RNA(tRNA)基因和8个核糖体RNA(rRNA)基因，检测到274个简单重复序列(SSR)，编码亮氨酸的密码子数量最多，编码色氨酸的密码子数量最少；川麦冬叶绿体基因组全长156 078 bp，GC总量37.8%，成功注释出85个蛋白编码基因，37个tRNA基因和8个rRNA基因，检测到265个SSR，编码亮氨酸的密码子数量最多，编码色氨酸的密码子数量最少；杭麦冬叶绿体基因组全长156 207 bp，GC总量37.7%，成功注释出85个蛋白编码基因，37个tRNA基因和8个rRNA基因，检测到274个SSR，编码亮氨酸的密码子数量最多，编码色氨酸的密码子数量最少。

结论：

系统发育树显示，与川麦冬相比，湖北麦冬与杭麦冬的亲缘关系更近。湖北麦冬、杭麦冬及川麦冬非编码区变异程度均大于编码区，叶绿体基因组可作为山麦冬属及沿阶草属植物物种鉴定的超级条形码。

Abstract

Objective:

To determine the chloroplast genomes of

Liriope spicata

var.

prolifera

Ophiopogon japonicus

in Sichuan and Zhejiang

analyze their sequence characteristics and complete the screening of specific DNA barcodes.

Method:

The chloroplast genomes of

spicata

var.

prolifera

japonicus

in Sichuan and Zhejiang were sequenced

spliced and annotated through high-throughtput sequencing technology

and the structural characteristics and phylogenetic relationships of chloroplast genomes were analyzed by bioinformatics.

Result:

The total length of chloroplast genome of

spicata

var.

prolifera

was 155 998 bp

the total content of guanine and cytosine (GC) was 37.7%

and 85 protein-coding genes

37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes were successfully annotated

a total of 274 simple sequence repeats (SSRs) were detected

the number of codons encoding leucine was the most

while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of

japonicus

in Sichuan province was 156 078 bp

the total content of GC was 37.8%

and 85 protein-coding genes

37 tRNA genes and 8 rRNA genes were successfully annotated

a total of 265 SSRs were detected

the number of codons encoding leucine was the most

while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of

japonicus

in Zhejiang province was 156 207 bp

the total content of GC was 37.7%

and 85 protein-coding genes

37 tRNA genes and 8 rRNA genes were successfully annotated

a total of 274 SSRs were detected with the highest number of codons encoding leucine and the lowest number of codons encoding tryptophan.

Conclusion:

The phylogenetic trees show that compared with

japonicus

in Sichuan province

spicata

var.

prolifera

is more closely related to

japonicus

in Zhejiang province. The variation of non-coding regions of

spicata

var.

prolifera

japonicus

in Zhejiang and Sichuan is greater than that in the coding region. The entire chloroplast genome can be used as a super barcode for identifying species of

Ophiopogon

and

Liriope

关键词

Keywords

references

F H WU , M T CHAN , D C LIAO , et al . Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers foridentification and breeding in Oncidiinae [J]． BMC Plant Biol ， 2010 ， 10 ( 1 )： 68 .

D Y KUANG , H WU , Y L WANG , et al . Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae)：implication for DNA barcoding and population genetics [J]． Genome ， 2011 ， 54 ( 8 )： 663 - 673 .

C J NOCK , D L WATERS , M A EDWARDS , et al . Chloroplast genome sequences from total DNA for plant identification [J]． Plant Biotechnol J ， 2011 ， 9 ( 3 )： 328 - 333 .

A TAKANO , H OKADA ． Phylogenetic relationships among subgenera，species，and varieties of Japanese Salvia L．(Lamiaceae) [J]． J Plant Res ， 2011 ， 124 ( 2 )： 245 - 252 .

高亚芳，刘莹莹，杨从卫，等．金铁锁叶绿体基因组序列及其系统发育分析 [J]．中草药， 2019 ， 50 ( 22 )： 5532 - 5536 .

左文明，曾阳，杨春芳，等．基于高通量技术的唐古特大黄叶绿体全基因组测序及应用研究 [J]．中草药， 2019 ， 50 ( 22 )： 5545 - 5553 .

W DONG , J LIU , J YU , et al . Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding [J]． PLoS One ， 2012 ， 7 ( 4 )： e35071 .

X LI , Y YANG , R J HENRY , et al . Plant DNA barcoding：from gene to genome [J]． Biol Rev Camb Philos Soc ， 2015 ， 90 ( 1 )： 157 - 166 .

国家药典委员会．中华人民共和国药典：一部 [M]．北京：中国医药科技出版社， 2015 ： 155 - 156 .

余伯阳，徐国钧．中药麦冬的资源利用研究 [J]．中草药， 1995 ， 26 ( 4 )： 205-210，225 .

简美玲，李荷，毛润乾．麦冬种质资源的研究进展 [J]．广东药科大学学报， 2011 ， 27 ( 5 )： 549 - 551 .

L C LI , Z W WANG , X P HU , et al . MDG-1 inhibits H 2 O 2 -induced apoptosis and inflammation in human umbilical vein endothelial cells [J]． Mol Med Rep ， 2017 ， 16 ( 3 )： 3673 - 3679 .

袁春丽，孙立，袁胜涛，等．麦冬有效成分的药理活性及作用机制研究进展 [J]．中国新药杂志， 2013 ， 22 ( 21 )： 2496 - 2502 .

李霞．麦冬多糖-1对心肌缺血再灌注大鼠内皮祖细胞与缺血修饰白蛋白变化的影响 [J]．中国老年学杂志， 2015 ， 35 ( 19 )： 5449 - 5450 .

J W ZHAO , D S CHEN , C S DENG , et al . Evalustion of anti-inflammatory activity of compounds isolated from the rhizome of Ophiopogon japonicus [J]． BMC Complement Altern Med ， 2017 ， 17 ( 1 )： 7 .

L Q BI , R ZHU , H KONG , et al . Ruscogenin attenuates monocrotaline-induced pulmonary hypertension in rats [J]． Int Immunopharmacol ， 2013 ， 16 ( 1 )： 7 - 16 .

M CHEN , Y H DU , M QUI , et al . Ophiopogonin B-induced autophagy in non-small cell lung cancer cells via inhibition of the PI3K/Akt signaling pathway [J]． Oncol Rep ， 2013 ， 29 ( 2 )： 430 - 436 .

M LIN , W SUN , W GONG , et al . Methylophiopogonanone A protects against cerebral ischemia/reperfusion injury and attenuates blood-brain barrier disruption in vitro [J]． PLoS One ， 2015 ， 10 ( 4 )： e0124558 .

Y ZHU , W CONG , L SHEN , et al . Fecal metabonomic study of a polysaccharide，MDG-1 from Ophiopogon japonicus on diabetic mice based on gas chromatography/time-of-flight mass spectrometry (GC TOF/MS) [J]． Mol Biosyst ， 2014 ， 10 ( 2 )： 304 - 312 .

X WANG , L SHI , S JOYCE , et al . MDG-1，a potential regulator of PPAR α and PPAR γ ，ameliorates dyslipidemia in mice [J]． Int J Mol Sci ， 2017 ， 18 ( 9 )： E1930 .

陈心启，马元俊．百合科药用新植物 [J]．植物科学学报， 1985 ， 3 ( 1 )： 25 - 27 .

国家质量监督检验检疫总局科技司．关于批准对襄麦冬实施地理标志产品保护的公告(2008年第53号) [EB/OL]． http://kjs.aqsiq.gov.cn/dlbzcpbhwz/ggcx/200805/t20080509_72032.html ， 2008-05-07/2019-12-04 .

刘霞，林韵涵，陈士林，等．道地药材川麦冬和浙麦冬的生态遗传分化 [J]．中国实验方剂学杂志， 2017 ， 23 ( 17 )： 27 - 33 .

胡仲义，吴帆，徐兵兵，等．不同地区麦冬遗传多样性的ISSR分析 [J]．中国野生植物资源， 2015 ， 34 ( 3 )： 23-26，33 .

许金榜，张君毅．山麦冬及其近缘种DNA条形码研究 [J]．植物研究， 2012 ， 32 ( 4 )： 452 - 457 .

J J DOYLE , J L DOYLE ． A rapid DNA isolation procedure for small quantities of fresh leaf tissue [J]． Phytochem Bull ， 1987 ， 19 ( 1 )： 11 - 15 .

J ZHOU , X CHEN , Y CUI , et al . Molecular structure and phylogenetic analyses of complete chloroplast genomes of two Aristolochia medicinal species [J]． Int J Mol Sci ， 2017 ， 18 ( 9 )： E1839 .

H JIANG , R LEI , S W DING , et al . Skewer：a fast and accurate adapter trimmer for next-generation sequencing paired-end reads [J]． BMC Bioinformatics ， 2014 ， 15 ： 182 .

G MARÇAIS , A L DELCHER , A M PHILLIPPY , et al . MUMmer4：a fast and versatile genome alignment system [J]． PLoS Comput Biol ， 2018 ， 14 ( 1 )： e1005944 .

D I HUANG , Q C B CRONK ． Plann：a command-line application for annotating plastome sequences [J]． Appl Plant Sci ， 2015 ， 3 ( 8 )： 1500026 .

M KEARSE , R MOIR , A WILSON , et al . Geneious Basic：an integrated and extendable desktop software platform for the organization and analysis of sequence data [J]． Bioinformatics ， 2012 ， 28 ( 12 )： 1647 - 1649 .

S KUMAR , G STECHER , M LI , et al . MEGA X：Molecular evolutionary genetics analysis across computing platforms [J]． Mol Biol Evol ， 2018 ， 35 ( 6 )： 1547 - 1549 .

S BEIBER , T THIEL , T MÜNCH , et al . MISA-web：a web server for microsatellite prediction [J]． Bioinformatics ， 2017 ， 33 ( 16 )： 2583 - 2585 .

K A FRAZER , L PACHTER , A POLIAKOV , et al . VISTA：computational tools for comparative genomics [J]． Nucleic Acids Res ， 2004 ， 32 ： W273 - W279 .

K KATOH , K KUMA , H TOH , et al . MAFFT version 5：improvement in accuracy of multiple sequence alignment [J]． Nucleic Acids Res ， 2005 ， 33 ( 2 )： 511 - 518 .

J G ZHOU , Y X CUI , X L CHEN , et al . Complete chloroplast genomes of Papaver rhoeas and Papaver orientale ：molecular structures，comparative analysis，and phylogenetic analysis [J]． Molecules ， 2018 ， 23 ( 2 )： E437 .

杨丽，赵韩生，彭镇华，等．竹子叶绿体基因组SSR分子标记的开发及应用 [J]．热带亚热带植物学报， 2014 ， 22 ( 3 )： 263 - 269 .

D Q TANG , J J LU , W FANG , et al . Development，characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species [J]． Mol Breeding ， 2010 ， 25 ( 2 )： 299 - 311 .

G I MCFADDEN ． Primary and secondary endosymbiosis and the origin of plastids [J]． J Phycol ， 2001 ， 37 ( 6 ) ： 951 - 959 .

C W JR BIRKY ． Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution [J]． Proc Natl Acad Sci USA ， 1995 ， 92 ( 25 )： 11331 - 11338 .

R K JANSEN , T A RUHLMAN ． Plastid Genomes of Seed Plants ： Genomics of Chloroplasts and Mitochondria [M]． Dordrecht ： Springer ， 2012 ， 35 ： 103 - 126 .

Y C HU , Q ZHANG , G Y RAO , et al . Occurrence of plastids in the sperm cells of Caprifoliaceae：biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance [J]． Plant Cell Physiol ， 2008 ， 49 ( 6 )： 958 - 968 .

R TESTOLIN , G CIPRIANI ． Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in the genus Actinidia [J]． Theor Appl Genet ， 1997 ， 94 ( 6/7 )： 897 - 903 .

张韵洁，李德铢．叶绿体系统发育基因组学的研究进展 [J]．植物分类与资源学报， 2011 ， 33 ( 4 ): 365 - 375 .

车晓彦，伍丕娥，周娟，等．麦冬药材TLC及HPLC特征图谱研究 [J]．药物分析杂志， 2012 ， 32 ( 12 ): 2262 - 2266 .

中国药材公司．中国常用中药材 [M]．北京：科学出版社， 1995 ： 286 .

M OEY , M LOHSE , B KREIKEMEYER , et al . Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic [J]． Plant J ， 2009 ， 57 ( 3 )： 436 - 445 .

M J HIBBERD , J P LINLEY , M S KHAN , et al . Transient expression of green fluorescent protein in various plastid types following microprojection bombardment [J]． Plant J ， 1998 ， 16 ( 5 )： 627 - 732 .

K E MCBRIDE , Z SVAB , D J SCHAAF , et al . Amplification of a chimeric Bacillus gene in chloroplast leads to an extraordinary level of an insecticidal protein tobacco [J]． Nat Biotechnol ， 1995 ， 13 ( 4 )： 362 - 365 .

R BOCK ． Genetic engineering of the chloroplast：novel tools and new application [J]． Curr Opin Biotechnol ， 2014 ， 26 ： 7 - 13 .

R BOCK ． Engineering plastid genomes：methods，tools，and application in basic research and biotechnology [J]． Annu Rev Plant Biol ， 2015 ， 66 ( 1 )： 211 - 241 .

J E BOYNTON , N W GILLHAM , E H HARRIS , et al . Chloroplast transformation in Chlamydomonas with high velocity microprojectiles [J]． Science ， 1988 ， 240 ( 4858 )： 1534 - 1538 .

Z SVAB , P HAJDUKIEWICZ , P MALIGA ． Stable transformation of plastids in higher plants [J]． Proc Natl Acad Sci USA ， 1990 ， 87 ( 21 )： 8526 - 8530 .

赵雅坤，史贤明，张忠明．人白细胞介素4在衣藻叶绿体中的高效转化及表达 [J]．华中农业大学学报， 2006 ， 25 ( 2 )： 110 - 116 .

林春晶，韦正乙，王云鹏，等．莴苣叶绿体转化体系的初步建立 [J]．农业生物与技术学报， 2014 ， 22 ( 4 )： 520 - 528 .

S KUMAR , A DHINGRA , H DANIELL ． Plastid expressed betaine aldehyde dehydrogenase gene in carrot cultured cells，roots and leaves confers enhanced salt tolerance [J]． Plant Physiol ， 2004 ， 136 ( 1 )： 2843 - 2854 .

S KUMAR , A DHINGRA , H DANIELL ． Manipulation of gene expression facilitates cotton plastid transformation of cotton by somatic embryogenesiss&maternal inheritance oftransgenes [J]． Plant Mol Biol ， 2004 ， 56 ( 2 )： 203 - 216 .

V A SIDOROV , D KASTEN , S Z PANG , et al . Technical advance：stable chloroplast transformation in potato：use of green fluorescent protein as a plastid marker [J]． Plant J ， 1999 ， 19 ( 2 )： 209 - 216 .

S RUF , M HERMANN , I BERGER , et al . Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit [J]． Nat Biotechnol ， 2001 ， 19 ( 9 )： 870 - 875 .

S M WHITNEY , T J ANDREWS ． Plastome-encoded bacterial ribulose-1，5-bisphosphate carboxylase/oxygenase (RubisCO) supports photosynthesis and growth in tobacco [J]． Proc Natl Acad Sci USA ， 2001 ， 98 ( 25 )： 14738 - 14743 .

王永飞，马三梅，王莹．高等植物叶绿体基因组转化的应用 [J]．遗传， 2004 ， 26 ( 6 )： 977 - 983 .

S H DING , Y ZHANG , Z HU , et al . mTERF5 acts as a transcriptional pausing factor to positively regulate transcription of chloroplast psbEFLJ [J]． Mol Plant ， 2019 ， 12 ( 9 )： 1259 - 1277 .

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⁰

Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang

DOI：10.13422/j.cnki.syfjx.20200947

摘要

Abstract

关键词

Keywords

references