Chloroplast Genomic Analysis of <italic style="font-style: italic">Pyrrosia assimilis</italic>

Chu-hong YANG; Ying-xian CUI; Li-ping NIE; Hui YAO; Yu WANG; Xia LIU

doi:10.13422/j.cnki.syfjx.20200747

您当前的位置：

首页 >

文章列表页 >

Chloroplast Genomic Analysis of Pyrrosia assimilis

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

- Chloroplast Genomic Analysis of Pyrrosia assimilis
- Chinese Journal of Experimental Traditional Medical Formulae Vol. 26, Issue 5, Pages: 123-131(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.中国医学科学院&北京协和医学院　药用植物研究所　国家中医药管理局中药资源保护重点研究室，北京　 100193
- 作者简介：
- 基金信息：
- DOI：10.13422/j.cnki.syfjx.20200747
  CLC： R22; Q732; R28; Q34; R931
- Received：04 November 2019，
  
  Published Online：17 December 2019，
  
  Published：05 March 2020
- 稿件说明：
移动端阅览
Chu-hong YANG, Ying-xian CUI, Li-ping NIE, et al. Chloroplast Genomic Analysis of Pyrrosia assimilis[J]. Chinese journal of experimental traditional medical formulae, 2020, 26(5): 123-131.
DOI：

Chu-hong YANG, Ying-xian CUI, Li-ping NIE, et al. Chloroplast Genomic Analysis of Pyrrosia assimilis[J]. Chinese journal of experimental traditional medical formulae, 2020, 26(5): 123-131. DOI： 10.13422/j.cnki.syfjx.20200747.

摘要

目的：

测定相近石韦

Pyrrosia assimilis

叶绿体基因组，分析其序列特征并探讨相近石韦本草基因组学研究。

方法：

应用高通量测序技术对相近石韦进行了叶绿体全基因组测序，利用生物信息学方法分析其结构特征和系统发育关系。

结果：

相近石韦叶绿体基因组呈环形双链结构，全长154 964 bp，鸟嘌呤和胞嘧啶(GC)总量41.2%；共注释到131个基因，包括88个蛋白编码基因，35个转运RNA(tRNA)基因和8个核糖体RNA(rRNA)基因；共检测到43个散在重复序列和56个简单重复序列(SSR)；编码亮氨酸的密码子使用频率最高，编码色氨酸的密码子数最少；叶绿体基因组全局比对分析筛选出5个高变异区(

psbA

，

rrn

16，

petA

psbJ

，

ndhC

trnM

和

psbM

petN

)；系统发育树显示相近石韦与波氏石韦

bonii

亲缘关系较近。

结论：

相近石韦叶绿体基因组中非编码区变异高于编码区，大单拷贝区(LSC)和小单拷贝区(SSC)变异大于反向重复区(IR)，筛选出的5个高变区可作为石韦属物种鉴定的候选DNA条形码。相近石韦的叶绿体基因组学研究为其他石韦属药用植物在分子鉴定、遗传基因转化、抗性蛋白表达及次生代谢途径解析等方面的研究提供了参考。

Abstract

Objective:

The complete chloroplast genome of

Pyrrosia assimilis

was sequenced

its sequence characteristics was analyzed and herbgenomics of

assimilis

was discussed.

Method:

Its complete chloroplast genome sequence was determined through high-throughput sequencing technology

and its structural characteristics and phylogenetic relationships were analyzed by bioinformatics.

Result:

The chloroplast genome of

assimilis

was a circular double-chain structure with a total length of 154 964 bp

and the total content of guanine and cytosine (GC) was 41.2%. A total of 131 genes were annotated

including 88 protein-coding genes

35 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. A total of 43 dispersed repetitive sequences and 56 simple sequence repeats (SSRs) were detected. The frequency of codon encoding leucine was the highest

while the number of codon encoding tryptophan was the lowest. Five highly divergent regions (

psbA

rrn

petA

psbJ

ndhC

trnM

and

psbM

petN

) were screened

phylogenetic analysis showed that

assimilis

was closely related to

bonii

Conclusion:

Comparative analysis of the complete chloroplast genome of

assimilis

reveals that non-coding regions exhibited a higher divergence than the coding regions

the large single copy region (LSC) and small single copy region (SSC) are more divergent than the reverse repeat region (IR)

the selected five highly variable regions can be used as specific DNA barcodes for identification of

Pyrrosia

species. Study on the chloroplast genome of

assimilis

can provide a reference for the molecular identification

genetic transformation

expression of resistance protein and secondary metabolism pathway analysis of other

Pyrrosia

medicinal plants.

关键词

Keywords

references

陈士林，宋经元．本草基因组学 [J]．中国中药杂志， 2016 ， 41 ( 21 ): 3881 - 3889 .

S L CHEN , J Y SONG , C SUN ， et al . Herbal genomics：examining the biology of traditional medicines [J]． Sciences ， 2015 ， 347 ( 6219 ): S27 - S29 .

陈士林．本草基因组学 [M]．北京：科学出版社， 2018 .

M WU , S LAN , B CAI ， et al . The complete chloroplast genome of Guadua angustifolia and comparative analyses of neotropical-paleotropical bamboos [J]． PLoS One ， 2015 ， 10 ( 12 ): e0143792 .

R K JANSEN , L A RAUBESON , J L BOORE ， et al . Methods for obtaining and analyzing whole chloroplast genome sequences [J]． Methods Enzymol ， 2005 ， 395 : 348 - 384 .

林小涵，刘志华，李卿，等．药用植物叶绿体基因组研究 [J]．世界科学技术—中医药现代化， 2010 ， 12 ( 3 ): 442 - 446 .

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

李滢，姚辉，宋经元，等．基于叶绿体全基因组的贝母属特异性DNA条形码的筛选 [J]．世界科学技术—中医药现代化， 2016 ， 18 ( 1 ): 24 - 28 .

李西文，胡志刚，林小寒，等．基于454FLX高通量技术的厚朴叶绿体全基因组测序及应用研究 [J]．药学学报， 2012 ， 47 ( 1 ): 124 - 130 .

J H LI , I MUTANDA , K B WANG ， et al . Chloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana [J]． Nat Commun ， 2019 ， 10 ( 1 ): 4850 .

韩丽颖，赵琳，牛野，等．石韦原植物、药材品种考证 [J]．中国民族民间医药， 2019 ， 28 ( 15 ): 16 - 20 .

文瑞良，伍兰．相异石韦性状及显微鉴别 [J]．中药材， 2000 ， 23 ( 8 ): 446 - 447 .

张雅琴，石钺，宋明，等．蕨类药材石韦及其混伪品的 psbA - trnH 序列鉴定 [J]．中国中药杂志， 2014 ， 39 ( 12 ): 2222 - 2226 .

S CAI , X CAI , S LI ， et al . The complete chloroplast genome of Pyrrosia bonii (Polypodiaceae)，an important ornamental and medical fern [J]． Mitochondrial DNA B ， 2018 ， 3 ( 2 ): 801 - 802 .

X WEI , Y QI , X ZHANG ， et al . Phylogeny，historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers [J]． Sci Rep ， 2017 ， 7 ( 1 ): 12757 .

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 .

K A FRAZER , L PACHTER , A POLIAKOV ， et al . Vista：computational tools for comparative genomics [J]． Nucleic Acids Res ， 2004 ， doi: 10.1093/nar/gkh458 http://dx.doi.org/10.1093/nar/gkh458 .

I PARK , S YANG , C GOYA ， et al . The complete chloroplast genome sequences of Aconitum pseudolaeve and Aconitum longecassidatum ，and development of molecular markers for distinguishing species in the Aconitum subgenus Lycoctonum [J]． Molecules ， 2017 ， 22 ( 11 ): E2012 .

Y JIAO , H M JIA , X W LI ， et al . Development of simple sequence repeat(SSR)markers from a genome survey of Chinese bayberry( Myrica rubra ) [J]． BMC Genomics ， 2012 ， 13 : 201 .

A H YANG , J J ZHANG , X H YAO ， et al . Chloroplast microsatellite markers in Liriodendron tulipifera (Magnoliaceae)and cross-species amplification in L . chinense [J]． Am J Bot ， 2011 ， 98 ( 5 ): e123 - e126 .

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 .

W POWELL , M MORGANTE , R MCDEVITT ， et al . Polymorphic simple sequence repeat regions in chloroplast genomes：applications to the population genetics of pines [J]． Proc Natl Acad Sci USA ， 1995 ， 92 ( 17 ): 7759 - 7763 .

J ZHOU , X CUI , X 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 .

Y MIN , S CAI , H XIAO ， et al . The complete chloroplast genome of Pyrrosia calvata (Polypodiaceae)，a traditional Chinese medicinal fern only restricted to Guangxi，China [J]． Mitochondrial DNA B ， 2019 ， 4 ( 1 ): 1757 - 1758 .

J XU , Y CHU , B LIAO ， et al . Panax ginseng genome examination for ginsenoside biosynthesis [J]． GigaScience ， 2017 ， 6 ( 11 ): 1 - 15 .

D ZHANG , W LI , E H XIA ， et al . The medicinal herb Panax notoginseng genome provides insights into ginsenoside biosynthesis and genome evolution [J]． Mol Plant ， 2016 ， 10 ( 6 ): 903 - 907 .

H XU , J SONG , H LUO ， et al . Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza [J]． Mol Plant ， 2016 ， 9 ( 6 ): 949 - 952 .

Z XU , R J PETERS , J WEIRATHER ， et al . Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis [J]． Plant J ， 2015 ， 82 ( 6 ): 951 - 961 .

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

X CHEN , J ZHOU , Y CUI ， et al . Identification of Ligularia herbs using the complete chloroplast genome as a super-barcode [J]． Front Pharmacol ， 2018 ， 9 : 695 .

马双姣，周建国，李滢，等．薯蓣和叉蕊薯蓣叶绿体基因组及特异性DNA条形码鉴定序列筛选研究 [J]．中国科学：生命科学， 2018 ， 48 ( 5 ): 571 - 582 .

P YANG , H ZHOU , J QIAN ， et al . The complete chloroplast genome sequence of Dendrobium officinale [J]. Mitochondrial DNA A DNA Mapp Seq Anal ， 2016 ， 27 ( 2 ): 1262 - 1264 .

J QIAN , J SONG , H GAO ， et al . The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza [J]． PLoS One ， 2013 ， 8 ( 2 ): e57607 .

钱雪艳，杨向东，郭东全，等．植物叶绿体遗传转化及研究进展 [J]．分子植物育种， 2008 ， 6 ( 5 ): 959 - 966 .

P T HAJDUKIEWICZ , L GILBERTSON , J M STAUB ， et al . Multiple pathways for Cre/lox-mediated recombination in plastids [J]． Plant J ， 2001 ， 27 ( 2 ): 161 - 170 .

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

S R SIKDAR , G SERINO , S CHAUDHURI ， et al . Plastid transformation in Arabidopsis thaliana [J]． Plant Cell Rep ， 1998 ， 18 ( 1/2 ): 20 - 24 .

S KUMAR , A DHINGRA , H DANIELL ． Plastid-expressed betaine aldehyde dehydrogen asegeneincal-qotcultured cell，sroots，and leaves confer senhanced salttolerance [J]． Plant Physiol ， 2004 ， 136 ( 1 ): 2843 - 2854 .

B K HOU , Y H ZHOU , L H WAN ， et al . Chloroplast transformation in oilseed rape [J]． Transgenic Res ， 2003 ， 12 ( 1 ): 111 - 114 .

何道一，夏仁杰，周秀杰，等．大豆 Lea 5基因过表达提高烟草抗旱和耐盐性的研究 [J]．激光生物学报， 2018 ， 27 ( 1 ): 53 - 59 .

高岩．拟南芥 fad 8基因在烟草叶绿体基因组表达研究 [D]．哈尔滨：哈尔滨师范大学， 2010 .

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 .

李胜男．三种石韦属植物的水分胁迫研究 [D]．长沙：中南林业大学， 2016 .

Z C XU , T Y XIN , D Bartels ， et al . Genome analysis of the ancient tracheophyte Selaginella tamariscina reveals evolutionary features relevant to the acquisition of desiccation tolerance [J]． Mol Plant ， 2018 ， 11 ( 7 ): 983 - 994 .

苏宁，孟昆，沈桂芳．植物叶绿体基因组基因表达调控的研究 [J]．生物技术通报， 1999 ( 1 ): 14 - 17 .

J M STAUB , B GARCIA , J GRAVES ， et al . High-yield production of a human therapeutic protein in tobacco chloroplasts [J]． Nat Biotechnol ， 2000 ， 18 ( 3 ): 333 - 338 .

侯丙凯，陈正华．苏云金芽孢杆菌杀虫蛋白基因克隆及油菜叶绿体遗传转化研究 [J]．遗传， 2001 ， 23 ( 1 ): 39 - 40 .

张中林，任延国，沈燕新，等．苏云金芽孢杆菌(Bt)晶体毒蛋白基因在烟草叶绿体中的表达 [J]．遗传学报， 2000 ， 27 ( 3 ): 270 - 277 .

杜美丽，刘秀明，江莺，等．叶绿体表达系统的研究进展 [J]．中国农学通报， 2011 ， 27 ( 9 ): 336 - 341 .

王金辉，李轶女，倪丕冲，等．叶绿体转化体系研究进展 [J]．生物技术通报， 2012 ( 1 ): 1 - 6 .

许柯，王玉伟，商艳芳．叶绿体基因组的转化研究 [J]．安徽农学通报， 2007 ， 13 ( 17 ): 29 - 30 .

肖钢，官春云．植物基因工程的新方向—叶绿体基因工程 [J]．作物研究， 2004 ( 5 ): 389 - 392 .

Views

下载量

CSCD

Alert me when the article has been cited

提交

Tools

Publicity Resources

Current Status and Prospect of Discipline Construction of Herbgenomics

Chloroplast Genome Structure of Stemona tuberosa and Phylogenetic Analysis Based on PacBio Sequencing

Identification and Quality Evaluation of Dendrobium flexicaule and Its Related Species

Top 10 Academic Progress of Traditional Chinese Medicine in 2021

Molecular Identification of Tibetan Codonopsis Plants Based on ITS2 and psbA-trnH Barcode

Related Author

Xue-qiong ZHANG

Hong-xi XU

Yi-fei LIU

Zhi-gang HU

Xia LIU

LIAN Yan

HUANG Feng

ZHU Wentao

Related Institution

School of Pharmacy, Hubei University of Chinese Medicine

School of Pharmacy, Shanghai University of Traditional Chinese Medicine

Sichuan Academy of Chinese Medicine Sciences

Key Laboratory of Standardization of Chinese Medicine， State Key Laboratory of Southwestern Chinese Medicine Resources， School of Pharmacy， Chengdu University of Traditional Chinese Medicine

Nanyang Vocational College of Agriculture

AI问答

Postal code：100700
Tel：010-84076882 Email：syfjx_2010@188.com
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备11006657号-10 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰

Chloroplast Genomic Analysis of Pyrrosia assimilis

DOI：10.13422/j.cnki.syfjx.20200747

摘要

Abstract

关键词

Keywords

references