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Article(id=1222469879035318545, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1222469875008790921, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2019-0564, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1563206400000, receivedDateStr=2019-07-16, revisedDate=1566748800000, revisedDateStr=2019-08-26, acceptedDate=null, acceptedDateStr=null, onlineDate=1769389131554, onlineDateStr=2026-01-26, pubDate=1573488000000, pubDateStr=2019-11-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1769389131554, onlineIssueDateStr=2026-01-26, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1769389131554, creator=13701087609, updateTime=1769389131554, updator=13701087609, issue=Issue{id=1222469875008790921, tenantId=1146029695717560320, journalId=1189982191388893191, year='2019', volume='54', issue='11', pageStart='1881', pageEnd='2140', issueExtLink='null', onlineDate='null', pubDate='1573488000000', pubDateStr='2019-11-12', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1769389130593, creator='13701087609', updateTime=1769389577080, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1222471747778109959, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1222469875008790921, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1222471747778109960, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1222469875008790921, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=2106, endPage=2112, ext={EN=ArticleExt(id=1222469879656075582, articleId=1222469879035318545, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

In order to explore the chloroplast genome characteristics of Sophora flavescens and the phylogenetic relationship of the genus, this study used high-throughput sequencing technology to sequence and functionally annotate the chloroplast genome of Sophora flavescens. The results showed that the full length 154 165 bp of Sophora flavescens chloroplast genome showed a typical four-stage structure. The chloroplast genome contains 123 genes, including 77 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Sequence analysis revealed 104 SSR loci, most of which consisted of A and T. In addition, the chloroplast genome codon preference is weak, and the coding region is biased towards the use of A and T bases. A comparative analysis of two different regions of Sophora flavescens chloroplast genome revealed four differential genes. Based on the maximum likelihood method (ML) for phylogenetic analysis of Sophora flavescens and 16 other leguminous, it was found that the relationship between Sophora flavescens and the genus Sophora alopecuroides is the closest. This study provides an important theoretical basis for the genetic variation, breeding and phylogenetic analysis of Sophora flavescens, and has certain reference value.

, authors=null, authorsList=Yong-gang QIAO, Jia-xin HE, Yong-fei WANG, Ya-ping CAO, Meng-jun JIA, Xin-rui ZHANG, Jian-ping LIANG, Yun SONG, authorCompany=null, correspAuthors=Yun SONG, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2019 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1222469882982158939, articleId=1222469879035318545, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=药用植物苦参的叶绿体基因组及其特征分析, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

为探究苦参叶绿体基因组特征及该属物种的系统进化发育关系，本研究利用高通量测序技术对苦参叶绿体基因组进行测序和功能注释。结果显示：苦参叶绿体基因组全长154 165 bp，呈典型的四段式结构。苦参叶绿体基因组共包含123个基因，包括77个蛋白编码基因、38个tRNA基因及8个rRNA基因。经序列分析鉴定出104个SSR位点，大部分重复由A和T组成。此外该叶绿体基因组密码子偏好性较弱，编码区偏向使用A和T碱基。对两个不同地区苦参叶绿体基因组进行比较分析发现了4个差异基因。基于最大似然法（ML）对苦参及其他16种豆科植物进行系统发育分析，发现苦参与其同属植物苦豆子的亲缘关系最近。本研究为苦参的遗传变异、育种以及系统发育分析等提供了重要的理论依据，具有一定的参考价值。

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*宋芸, Tel: 13835441175, E-mail:
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PLoS One, 2010, 5: e12762., articleTitle=The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.), refAbstract=null)], funds=[Fund(id=1222469891735670950, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, awardId=2018ZDGH0101, language=CN, fundingSource=山西振东企业国际合作项目资助(2018ZDGH0101), fundOrder=null, country=null), Fund(id=1222469891815362731, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, awardId=J2015028, language=CN, fundingSource=山西省高等学校教学改革项目资助(J2015028), fundOrder=null, country=null), Fund(id=1222469891916026035, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, awardId=J2017031, language=CN, fundingSource=山西省高等学校教学改革项目资助(J2017031), fundOrder=null, country=null), Fund(id=1222469892033466553, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, awardId=201801D121204, language=CN, fundingSource=山西省基础研究计划资助(201801D121204), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1222469883326091905, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, xref=null, ext=[AuthorCompanyExt(id=1222469883334480516, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, companyId=1222469883326091905, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China), AuthorCompanyExt(id=1222469883338674820, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, companyId=1222469883326091905, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=山西农业大学生命科学学院, 山西 太谷 030801)])], figs=[ArticleFig(id=1222469889764347933, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=iNdCp72O70T/M0zusRMVFQ==, figureFileBig=1CHsUJYzuhSbaUjfAwYvmg==, tableContent=null), ArticleFig(id=1222469889885982756, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Figure 1, caption= Chloroplast genome map of <i>Sophora flavescens</i>. Genes drawn inside the circle are transcribed clockwise, genes outside are transcribed counter clockwise. Genes are color coded by their function in the legend. The area in darker gray and lighter gray in the inner circle indicates GC content and AT content, respectively , figureFileSmall=iNdCp72O70T/M0zusRMVFQ==, figureFileBig=1CHsUJYzuhSbaUjfAwYvmg==, tableContent=null), ArticleFig(id=1222469890141835314, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=sxqXrF9znSuyOV5Ku741eA==, figureFileBig=nNKiIz0LMDm5ABPOVdcdjw==, tableContent=null), ArticleFig(id=1222469890263470138, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Figure 2, caption= SSR distribution of <i>Sophora flavescens</i> chloroplast genome. A: Distribution of SSR in the coding region, intron region, and intergenic region of the gene; B: Distribution of various types of SSRs in LSC, SSC and IR regions , figureFileSmall=sxqXrF9znSuyOV5Ku741eA==, figureFileBig=nNKiIz0LMDm5ABPOVdcdjw==, tableContent=null), ArticleFig(id=1222469890389299266, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=IKni6hC4/E0XywN71OgQ3g==, figureFileBig=4GnxRouldH2fS8SFCLm+Dw==, tableContent=null), ArticleFig(id=1222469890519322697, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Figure 3, caption= Relative synonymous codon usage of <i>Sophora flavescens</i> chloroplast genome. The value of the relative synonymous codon usage (RSCU > 1) is shown in underline , figureFileSmall=IKni6hC4/E0XywN71OgQ3g==, figureFileBig=4GnxRouldH2fS8SFCLm+Dw==, tableContent=null), ArticleFig(id=1222469890607403089, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=KbZqmAl1ReKv2otJvCQCWw==, figureFileBig=afAxglj30mbvAM/enT2qhw==, tableContent=null), ArticleFig(id=1222469890779369561, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Figure 4, caption= Comparison of chloroplast genomes of <i>Sophora flavescens</i> in different regions. A: <i>Sophora flavescens</i> that have been sequenced in this study; B: <i>Sophora flavescens</i> in another different region , figureFileSmall=KbZqmAl1ReKv2otJvCQCWw==, figureFileBig=afAxglj30mbvAM/enT2qhw==, tableContent=null), ArticleFig(id=1222469890905198690, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=/9dY1RcUa8r3rYKSwkbwkw==, figureFileBig=2Z5M/ESBAol/e6CbioCYKg==, tableContent=null), ArticleFig(id=1222469891010056304, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Figure 5, caption= The phylogenetic tree was constructed based on the chloroplast genome of 17 legumes using the maximum likelihood method , figureFileSmall=/9dY1RcUa8r3rYKSwkbwkw==, figureFileBig=2Z5M/ESBAol/e6CbioCYKg==, tableContent=null), ArticleFig(id=1222469891089748090, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Genome feature Sophora flavescens
Size/bp 154 165
Number of gene 123
Protein-coding genes 77
tRNA genes 38
rRNA genes 8
GC content 36.5%
GC content in LSC 34.1%
GC content in SSC 30.1%
GC content in IR 42.7%
), ArticleFig(id=1222469891190411391, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Table 1, caption=

Statistics on the chloroplast gene annotation of Sophora flavescens

, figureFileSmall=null, figureFileBig=null, tableContent=
Genome feature Sophora flavescens
Size/bp 154 165
Number of gene 123
Protein-coding genes 77
tRNA genes 38
rRNA genes 8
GC content 36.5%
GC content in LSC 34.1%
GC content in SSC 30.1%
GC content in IR 42.7%
), ArticleFig(id=1222469891265908869, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Function Family name KS
Photosynthesis Subunits of ATP synthase atpA, atpB, atpE, atpF*, atpH, atpI
Subunits of NADH dehydrogenase ndhA*, ndhB*, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome petA, petB, petD, petG, petL, petN
Subunits of photosystem Ⅰ psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem Ⅱ psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
Subunit of rubisco rbcL
Self-replication Large subunit of ribosome rpl2*, rpl14, rpl16, rpl20, rpl23, rpl32, rpl33, rpl36
DNA dependent RNA polymerase rpoA, rpoB, rpoC1*, rpoC2
Small subunit of ribosome rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps18, rps19
rRNA Genes rrn16
tRNA Genes trnA-UGC*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnH-GUG,
trnI-CAU, trnI-GAU*, trnK-UUU*, trnL-CAA, trnL-UAA*, trnL-UAG, trnM-CAU,
trnN-GUU, trnP-GGG, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU,
trnS-GGA, trnS-UGA, trnT-CGU*, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC*,
trnW-CCA, trnY-GUA
Other genes Acety1-CoA carboxylase accD
c-type cytochrom synthesis gene ccsA
Envelop membrane protein cemA
Protease clpP*
Maturase matK
Unknown Conserved open reading frames ycf2, ycf3*, ycf4
), ArticleFig(id=1222469891395932305, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Table 2, caption=

Functional classification of Sophora flavescens chloroplast gene. *Indicate the intron-containing genes

, figureFileSmall=null, figureFileBig=null, tableContent=
Function Family name KS
Photosynthesis Subunits of ATP synthase atpA, atpB, atpE, atpF*, atpH, atpI
Subunits of NADH dehydrogenase ndhA*, ndhB*, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome petA, petB, petD, petG, petL, petN
Subunits of photosystem Ⅰ psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem Ⅱ psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
Subunit of rubisco rbcL
Self-replication Large subunit of ribosome rpl2*, rpl14, rpl16, rpl20, rpl23, rpl32, rpl33, rpl36
DNA dependent RNA polymerase rpoA, rpoB, rpoC1*, rpoC2
Small subunit of ribosome rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps18, rps19
rRNA Genes rrn16
tRNA Genes trnA-UGC*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnH-GUG,
trnI-CAU, trnI-GAU*, trnK-UUU*, trnL-CAA, trnL-UAA*, trnL-UAG, trnM-CAU,
trnN-GUU, trnP-GGG, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU,
trnS-GGA, trnS-UGA, trnT-CGU*, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC*,
trnW-CCA, trnY-GUA
Other genes Acety1-CoA carboxylase accD
c-type cytochrom synthesis gene ccsA
Envelop membrane protein cemA
Protease clpP*
Maturase matK
Unknown Conserved open reading frames ycf2, ycf3*, ycf4
), ArticleFig(id=1222469891517567129, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Parameter T3s C3s A3s G3s Nc GC3s
Value 0.398 9 0.237 2 0.410 8 0.234 5 55.34 0.354
), ArticleFig(id=1222469891626619040, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1222469879035318545, language=CN, label=Table 3, caption=

Overall characteristics of codon usage of Sophora flavescens chloroplast genome

, figureFileSmall=null, figureFileBig=null, tableContent=
Parameter T3s C3s A3s G3s Nc GC3s
Value 0.398 9 0.237 2 0.410 8 0.234 5 55.34 0.354
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药用植物苦参的叶绿体基因组及其特征分析
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乔永刚 , 贺嘉欣 , 王勇飞 , 曹亚萍 , 贾孟君 , 张鑫瑞 , 梁建萍 , 宋芸 *
药学学报 | 研究论文 2019,54(11): 2106-2112
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药学学报 |研究论文 2019 , 54 (11) : 2106 -2112
药用植物苦参的叶绿体基因组及其特征分析
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乔永刚, 贺嘉欣, 王勇飞, 曹亚萍, 贾孟君, 张鑫瑞, 梁建萍, 宋芸*
作者信息
  • 山西农业大学生命科学学院, 山西 太谷 030801
通讯作者:
*宋芸, Tel: 13835441175, E-mail:
Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens
Yong-gang QIAO, Jia-xin HE, Yong-fei WANG, Ya-ping CAO, Meng-jun JIA, Xin-rui ZHANG, Jian-ping LIANG, Yun SONG*
Affiliations
  • College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
出版时间: 2019-11-12 doi: 10.16438/j.0513-4870.2019-0564
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摘要
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为探究苦参叶绿体基因组特征及该属物种的系统进化发育关系，本研究利用高通量测序技术对苦参叶绿体基因组进行测序和功能注释。结果显示：苦参叶绿体基因组全长154 165 bp，呈典型的四段式结构。苦参叶绿体基因组共包含123个基因，包括77个蛋白编码基因、38个tRNA基因及8个rRNA基因。经序列分析鉴定出104个SSR位点，大部分重复由A和T组成。此外该叶绿体基因组密码子偏好性较弱，编码区偏向使用A和T碱基。对两个不同地区苦参叶绿体基因组进行比较分析发现了4个差异基因。基于最大似然法（ML）对苦参及其他16种豆科植物进行系统发育分析，发现苦参与其同属植物苦豆子的亲缘关系最近。本研究为苦参的遗传变异、育种以及系统发育分析等提供了重要的理论依据，具有一定的参考价值。

苦参  /  叶绿体基因组  /  SSR  /  密码子偏好性  /  比较基因组学  /  系统发育分析

In order to explore the chloroplast genome characteristics of Sophora flavescens and the phylogenetic relationship of the genus, this study used high-throughput sequencing technology to sequence and functionally annotate the chloroplast genome of Sophora flavescens. The results showed that the full length 154 165 bp of Sophora flavescens chloroplast genome showed a typical four-stage structure. The chloroplast genome contains 123 genes, including 77 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Sequence analysis revealed 104 SSR loci, most of which consisted of A and T. In addition, the chloroplast genome codon preference is weak, and the coding region is biased towards the use of A and T bases. A comparative analysis of two different regions of Sophora flavescens chloroplast genome revealed four differential genes. Based on the maximum likelihood method (ML) for phylogenetic analysis of Sophora flavescens and 16 other leguminous, it was found that the relationship between Sophora flavescens and the genus Sophora alopecuroides is the closest. This study provides an important theoretical basis for the genetic variation, breeding and phylogenetic analysis of Sophora flavescens, and has certain reference value.

Sophora flavescens  /  chloroplast genome  /  SSR  /  codon preference  /  comparative genomics  /  phylogenetic analysis
乔永刚, 贺嘉欣, 王勇飞, 曹亚萍, 贾孟君, 张鑫瑞, 梁建萍, 宋芸. 药用植物苦参的叶绿体基因组及其特征分析. 药学学报, 2019 , 54 (11) : 2106 -2112 . DOI: 10.16438/j.0513-4870.2019-0564
Yong-gang QIAO, Jia-xin HE, Yong-fei WANG, Ya-ping CAO, Meng-jun JIA, Xin-rui ZHANG, Jian-ping LIANG, Yun SONG. Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens[J]. Acta Pharmaceutica Sinica, 2019 , 54 (11) : 2106 -2112 . DOI: 10.16438/j.0513-4870.2019-0564
正文
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苦参(Sophora flavescens Ait.)为豆科槐属(Sophora)多年生落叶亚灌木或多年生草本植物[1], 其干燥根入药, 具有清热、燥湿、杀虫、利尿等功效[2]。苦参的主要化学成分为奎诺里西啶生物碱和黄酮类化合物[3], 苦参除用于中药方剂外, 还是制药工业中常用的制剂、日用品、生物农药和兽药的主要原料, 如:苦参碱注射液[4]、苦参碱滴眼液[5]、苦参碱杀虫剂[6]等。
叶绿体是细胞内半自主性的细胞器, 自身拥有相对独立的遗传物质, 即叶绿体基因组。叶绿体基因组所包含的遗传信息虽远小于核基因组, 但叶绿体基因组结构稳定、高度保守[7], 在植物系统发育、物种鉴定和遗传转化等研究中都具有重要意义[8-12]。近年来, 随着测序技术的发展和叶绿体基因组生物信息学分析技术的成熟, 叶绿体基因组的研究也得到了迅速发展。自1986年首次测序获得烟草(Nicotiana tabacum)[13]和地钱(Marchantia polymorpha)[14]叶绿体基因组的完整序列以来, 叶绿体基因组数据库迅速增加充实。之后, 不断有新物种的叶绿体基因组被测得。叶绿体基因组多是环式双链结构, 典型的环式双链叶绿体基因组结构包括4个部分:大单拷贝区(large single copy, LSC)和小单拷贝区(small single copy, SSC), 以及两个反向重复区(inverted repeats, IRs)将其分隔开[15]。
目前已有多种豆科植物的叶绿体基因组被报道[16-18], Zhang等[19]对苦参叶绿体基因组测序并进行遗传进化分析, 但并未对其叶绿体基因组进行详细论述。本研究通过对苦参叶绿体基因组测序, 从SSR、密码子偏好性、比较基因组学等方面对其进行分析, 以期为苦参的遗传变异、育种以及豆科植物的系统进化发育和药用植物的分子系统发育提供重要的理论基础和依据。
材料与方法
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材料  本研究所用苦参种植于山西农业大学生命科学学院药用植物园, 于2018年7月选取一年生植株的新鲜叶片, 液氮速冻后于-80 ℃保存备用。
DNA的提取、测序  用改良的CTAB法提取叶片DNA, 琼脂糖凝胶电泳和NANODROP 2000C (Thermo Fisher Scientific, 美国)检测DNA质量和浓度。DNA检测合格后, 用机械打断(超声波)的方法将DNA片段化, 经过片段纯化、末端修复、3'端加A、连接测序接头, PCR扩增等获得测序文库, 质检合格后用Illumina HiSeq (陕西博瑞德生物科技有限公司)进行测序。
叶绿体基因组的注释和比较基因组学分析  运用MITObim软件[20]对叶绿体基因组进行组装, 参考序列为Sophora alopecuroides L. (NC_036102), 将获得的叶绿体基因组用GeSeq软件[21]进行基因注释并将最终结果提交至GenBank (MN205931)。利用OGDRAW在线软件[22]绘制苦参叶绿体基因组图谱, 并比较和分析两个不同地区苦参的叶绿体基因组。
SSR分析  利用MISA软件[23]对苦参Unigene序列进行分析, 参数设置为:单核苷酸重复次数 > 10, 二核苷酸重复次数 > 6, 三核苷酸、四核苷酸、五核苷酸和六核苷酸重复次数 > 5; 2个SSR之间的最小距离设置为100 bp。
密码子偏好性分析  苦参叶绿体基因组的密码子组成分析运用软件CodonW1.4.2 (availableonline: downloads.fyxm.net/CodonW-76666.html)[24], 获得相关参数:有效密码子数(effective number of codon, Nc)、相对同义密码子使用情况(relative synonymous codon usage, RSCU)、GC含量和第三位上的GC碱基的含量(GC3s)。
系统发育分析  利用BioEdit软件[25]对17个豆科物种的叶绿体基因组序列进行比对, 将比对结果采用MEGA7.0软件[26]ML法构建系统进化树。
结果与分析
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1 叶绿体基因组的基本特征
采用Illumina HiSeq高通量测序平台对苦参叶绿体基因组测序, 经过测序质量控制[27], 样品Q30碱基百分比不小于90%, 利用MITObim软件对其组装得到苦参的叶绿体全基因组。苦参的叶绿体基因组呈现典型的四段式结构(图 1), 包括大单拷贝区(LSC)、小单拷贝区(SSC), 以及两个大小相同、方向相反的反向重复区(IRA, IRB)。
苦参的叶绿体基因组全长154 165 bp (表 1), 其中LSC、SSC、IR区域分别为84 413 bp、18 056 bp、51 696 bp, GC含量为36.5%, 其中LSC和SSC区域分别为34.1%、30.1%, 而IR区域的GC含量为42.7%。苦参叶绿体基因组的基因含量和序列较为保守, 共注释123个基因(表 2), 包括77个蛋白质编码基因(62.6%)、38个tRNA基因(30.9%)以及8个rRNA基因(6.5%)。按照功能可将这些基因分为4类:其中atpA、ndhB、psaI、rbcL等44个基因与光合作用相关; rpl2、rps2、trnA-UGC等57个基因与自我复制相关; 还有其他基因和功能未知的基因。其中有13个基因含有内含子, ycf3、clpP以及trnI-GAU含有两个内含子。
2 SSR位点分析
利用MISA软件对苦参Unigene序列进行分析, 共检测到104个SSR位点, 大部分的SSR位于基因间隔区(intergenic spacer, IGS), 共有84个(80.77%); 而分布于基因编码区(coding sequence, CDS)的SSR最少, 只有7个(6.73%) (图 2A)。同时发现大部分的SSR均位于LSC区域内, 只有少数位于SSC和IR区域内, 其中位于IR区的SSR最少。SSR位点包括单核苷酸重复、双核苷酸重复、三核苷酸重复、四核苷酸重复以及复合SSR。其中单核苷酸重复最多, 主要分布在LSC区域, 而三核苷酸重复和四核苷酸重复数量最少, 分布于LSC区域内(图 2B)。苦参叶绿体基因组中的SSR主要是由A和T组成的, 其中大部分是以A/T碱基构成的单核苷酸重复, 共检测到73条, 其次是AT/AT组成的二核苷酸重复序列, 二者合计占所有重复序列的90%以上。
3 密码子偏好性分析
利用CodonW1.4.2对苦参叶绿体基因组的密码子组成进行分析。结果表明(表 3), 苦参叶绿体基因组的Nc值为55.34, 说明该叶绿体基因组的密码子偏好性较弱。苦参叶绿体基因组的GC3s含量为35.4%, GC含量也小于50%, 说明苦参叶绿体基因的密码子偏向使用A和T这两种碱基。对苦参叶绿体基因组的RSCU进行分析(图 3), RSCU > 1的密码子有32个, 其中以A/T碱基结尾的有27个, 占84.38%, 表明这些密码子偏向以A/T结尾。
4 比较基因组学分析
将已测序苦参叶绿体基因组作为参考, 与贵阳地区的苦参叶绿体基因组序列[19]进行相似性比较分析(图 4)。结果表明, 两个不同地区苦参叶绿体基因组序列整体上高度相似, 但其仍存在明显差异。二者的叶绿体基因组长度不同, 相差213 bp, 且其在LSC区和IR区有明显区别, 主要表现为petB、petD、rpl16和rps12等基因的扩张和收缩。在两个叶绿体基因组的LSC/IR和SSC/IR边界区, 由于IR区正常拷贝时的不完整, 产生了rps19和ycf1两个假基因。其中rps19基因正好位于IRb/LSC边界区并截止于LSC区。而ycf1基因位于IR/SSC边界区, 横跨了IR区和SSC区。
5 系统发育分析
为了鉴定苦参在豆科中的进化位置, 本研究以苦参叶绿体基因组和已公布的16种豆科植物叶绿体基因组序列为研究对象, 利用BioEdit软件对17个物种的叶绿体全基因组序列进行比对, 将比对结果采用MEGA7.0软件ML法(maximum likelihood, 最大似然法)构建系统进化树(图 5)。结果显示, 苦参与同属植物苦豆子(Sophora alopecuroides L.)的亲缘关系最近, 二者的遗传距离为0.019。同时位于山黧豆属的大山黧豆(Lathyrus davidii)与其他16个物种的亲缘关系最远, 遗传距离均大于0.75, 为单系分支。
讨论
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苦参是一种重要的药用植物, 但是目前对苦参叶绿体基因组方面的研究还很有限。而叶绿体基因组高度保守, 含有大量的遗传信息, 对研究苦参的遗传变异、育种及该科、属内物种的系统进化发育等具有重要意义。
本研究通过测序获得苦参叶绿体基因组序列, 并对其进行分析。SSR位点分析对研究苦参的物种进化、遗传和变异具有重要的意义[28]。经分析共鉴定出104个SSR, 多分布于LSC区, 主要由碱基A和T组成。由于AT键相对于GC键少了一个氢键, 其断裂所需的能量远小于GC键, 相对于GC键而言更易断裂发生变动, 因此在叶绿体基因组中含AT重复基序结构的SSR重复类型出现的可能性更大, 这与Kuang和Qian等的研究结果一致[29, 30]。大部分的SSR位于IGS区, 而分布于CDS区的SSR最少, 这是由于生物体的外显子区域相对较保守, 而内含子区和非编码区的保守性比外显子区要弱, 因此SSR在这两个区域出现的可能性增加[31]。
对苦参叶绿体基因组的密码子进行分析, 获得相关参数Nc、RSCU、GC和GC3s。Nc值的范围在20~61之间, 越靠近20表明密码子的偏好性越强, 反之, 越偏向61密码子的偏好性越弱[32]。经分析发现苦参叶绿体基因组的Nc值大于40, 说明苦参叶绿体基因组的密码子使用偏好性较弱。RSCU=1, 表明该密码子的使用没有偏好性, RSCU > 1, 说明该密码子的使用频率较高, 反之则较低[33]。发现RSCU > 1的密码子更多, 且偏向以A/T结尾。GC和GC3s含量在密码子的偏好性分析中也具有重要意义, 经测定苦参叶绿体基因组的GC含量和GC3s含量均小于50%, 说明苦参叶绿体基因组的密码子偏好使用A和T碱基。
植物叶绿体基因组的扩张和收缩是植物比较基因组学中的重要数据, 它们被认为是叶绿体基因组变异的主要机制[34, 35]。本研究对两个不同地区的苦参叶绿体基因组进行比较分析, 发现二者的叶绿体基因组序列整体上高度相似, 但其仍存在明显差异, 主要表现为petB、petD、rpl16和rps12等基因的扩张和收缩。根据这些基因区域的变化可进行DNA条形码的开发, 有望利用DNA条形码区分不同地区苦参, 以此来优化苦参种质资源并进行苦参的良种繁育。基于整个叶绿体基因组的系统发育分析显示, 苦参与同属的苦豆子的亲缘关系最近。利用叶绿体基因组可为解决豆科槐属内植物的分类问题提供参考, 但是已发表的槐属植物叶绿体基因组数据有限, 因此, 还需要获得更多槐属植物的叶绿体基因组才能更好的研究该属植物的系统发育关系。
结论
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本文通过对苦参叶绿体基因组进行测序、注释、分析和预测, 获得其全长154 165 bp, 共注释到123个基因, 筛选了104个SSR位点。同时分析发现其基因组密码子偏好性较弱。与另一不同地区苦参叶绿体基因组进行比较分析后, 发现二者在LSC区有较大差异。经系统进化分析可知, 苦参与同属植物苦豆子的亲缘关系最近。本研究对苦参的系统进化发育以及遗传变异、育种等方面都具有重要作用, 同时也为苦参和叶绿体基因组未来的研究奠定了重要基础。
基金
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  • 山西振东企业国际合作项目资助(2018ZDGH0101)
  • 山西省高等学校教学改革项目资助(J2015028)
  • 山西省高等学校教学改革项目资助(J2017031)
  • 山西省基础研究计划资助(201801D121204)
文献
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2019年第54卷第11期
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doi: 10.16438/j.0513-4870.2019-0564
  • 接收时间：2019-07-16
  • 首发时间：2026-01-26
  • 出版时间：2019-11-12
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  • 收稿日期：2019-07-16
  • 修回日期：2019-08-26
基金
山西振东企业国际合作项目资助(2018ZDGH0101)
山西省高等学校教学改革项目资助(J2015028)
山西省高等学校教学改革项目资助(J2017031)
山西省基础研究计划资助(201801D121204)
作者信息
    山西农业大学生命科学学院, 山西 太谷 030801

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*宋芸, Tel: 13835441175, E-mail:
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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