Article(id=1236337182865150732, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1236337182303113996, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2023.06.003, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1655740800000, receivedDateStr=2022-06-21, revisedDate=1659456000000, revisedDateStr=2022-08-03, acceptedDate=null, acceptedDateStr=null, onlineDate=1772695354429, onlineDateStr=2026-03-05, pubDate=1687622400000, pubDateStr=2023-06-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1772695354429, onlineIssueDateStr=2026-03-05, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1772695354429, creator=13701087609, updateTime=1772695354429, updator=13701087609, issue=Issue{id=1236337182303113996, tenantId=1146029695717560320, journalId=1235980609244409860, year='2023', volume='44', issue='6', pageStart='1083', pageEnd='1305', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1772695354295, creator=13701087609, updateTime=1772695447813, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1236337574608950114, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1236337182303113996, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1236337574613144419, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1236337182303113996, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=1097, endPage=1105, ext={EN=ArticleExt(id=1236337183125197583, articleId=1236337182865150732, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Genomic Characteristics and Phylogenic Analysis of Chloroplast of the Endangered Plant Paphiopedilum venustum, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Paphiopedilum venustum, an endangered wild resources, has high ornamental value and conservation biological value. Chloroplast genome (cpDNA), small with stable structure and high conserved in nature, has been widely used in plant phylogeny and species identification. Understanding the chloroplast genome structure of P. venustum is of great significance in revealing the phylogenetic relationship of Paphiopedilum. In this study, the whole chloroplast genome of P. venustum was sequenced by the Illumina sequencing technology, the chloroplast genome was annotated using GeSeq, BLAST and hmmer, the genome structure, gene number, repeats, codon usage bias, phylogenetic development were analyzed using the bioinformatics softwares such as MISA, codonW and Fasttree. The chloroplast genome of P. venustum had a conserved quadripartite structure, with a pair of inverted repeats (IRs) separated a large single copy (LSC) region and a small single copy (SSC) region from the small single-copy region (SSC), with a total length of 158 298 bp. The guanine and cytosine (GC) content of chloroplast protein coding genes was 35.4%, and 129 genes were annotated, including 79 protein coding genes, 38 tRNA genes, 8 rRNA genes, and 4 pseudogenes. 78 simple sequence repeat (SSR) loci were detected, most of which were mononucleotide repeats and dinucleotide repeats, accounting for 84.62% and 10.26% respectively. There were no pentanucleotide repeats, and most of the repeats were composed of A or T base. 32 high-frequency codons were identified, and 90.6% of them ended in A or U, preferred codons ending in A or U. The codon encoding leucine (Leu) had the highest frequency of use, while the codon encoding cysteine (Cys) had the lowest frequency of use. Phylogenetic tree was constructed by comparing the chloroplast genomes of 18 orchidaceae plants. It was found that the two species of Cypripedilum calceolus and C. tibeticum were separated from 16 species of Paphiopedilum and clustered into a single branch, and the genus of Paphiopedilum was divided into two groups, among which P. venustum and P. purpuratum were closely related. SSR and nucleotide polymorphisms can be used as molecular markers for germplasm identification and genetic diversity analysis of Paphiopedilum, which could provide a theoretical basis for germplasm identification and phylogeny of rare and endangered plant Paphiopedilum and its relatives, and lay a foundation for population restoration, biodiversity protection, innovative utilization and new variety breeding of Paphiopedilum.

, correspAuthors=Xiuling LI, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, 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, authorCompany=null, fund=null, authors=null, authorsList=Jizheng FAN, Xiuling LI, Mingzhi LI, Zhaoyang BU, Jingzhou HE, Yanhua ZENG), CN=ArticleExt(id=1236337183347495699, articleId=1236337182865150732, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=濒危植物秀丽兜兰叶绿体基因组特征与系统发育分析, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

秀丽兜兰（Paphiopedilum venustum）具有较高的观赏价值和保护生物学价值，野外资源濒临灭绝，叶绿体基因组（cpDNA）具有基因组小、结构稳定、高度的保守性等优点被广泛用于植物系统发育和物种鉴定，了解秀丽兜兰的叶绿体基因组结构，对揭示兜兰属植物的系统进化关系具有重要意义。本研究通过二代高通量测序技术获得秀丽兜兰叶绿体全基因组序列，利用GeSeq、blast和hmmer软件对叶绿体基因组进行注释，采用MISA、CodonW、fasttree等生物信息学软件对其基因组结构、基因数目、序列重复、密码子偏好性和系统发育进行分析。结果表明：秀丽兜兰叶绿体基因组结构保守，具有典型的环状四分体结构，一对反向重复区（IRs）将大单拷贝区（LSC）和小单拷贝区（SSC）分开，全长158 298 bp，GC含量为35.4%，共注释得到129个基因，包括79个蛋白编码基因，38个tRNA基因、8个rRNA基因和4个假基因；检测到78个SSR位点，以单核苷酸重复和二核苷酸重复为主，分别占84.62%和10.26%，无五核苷酸重复，并且大多由A或T构成；确定了高频密码子32个，90.6%都以A或U结尾，编码亮氨酸（Leu）的密码子使用频率最高，而编码半胱氨酸（Cys）的密码子使用频率最低。通过比较18个兰科植物叶绿体基因组，构建系统进化树发现，紫花杓兰和西藏杓兰2个杓兰属植物被单独聚成一支，兜兰属被分成两大类，其中秀丽兜兰（P. venustum）与同属的紫纹兜兰（P. purpuratum）亲缘关系密切。本研究筛选出的SSR和核苷酸多态性能够作为兜兰属植物种质鉴定和遗传多样性的分子标记，可为珍稀濒危植物秀丽兜兰及其近缘种的种质鉴定、系统发育等提供理论依据，为兜兰属植物种群恢复、生物多样性保护、创新利用及新品种选育奠定基础。

, correspAuthors=李秀玲, authorNote=null, correspAuthorsNote=, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=l/7mcN0R0Hor4ySv8UQVIQ==, magXml=fieUK6wWSPVyvOB5EafO+Q==, pdfUrl=null, pdf=qkkq6L11gsmrmylmGNmidA==, pdfFileSize=1854908, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=K7Z4Am+V9ztiZihoI2514A==, mapNumber=null, authorCompany=null, fund=null, authors=, authorsList=范继征, 李秀玲, 李明智, 卜朝阳, 何荆洲, 曾艳华)}, authors=[Author(id=1236337183834034976, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1236337182865150732, orderNo=0, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1236337183922115366, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1236337182865150732, authorId=1236337183834034976, language=EN, stringName=Jizheng FAN, firstName=Jizheng, middleName=null, lastName=FAN, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=¹, address=^1.Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1236337184022778665, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1236337182865150732, authorId=1236337183834034976, language=CN, stringName=范继征, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=¹, address=^1.广西农业科学院花卉研究所，广西南宁　530007, bio={"content":"

范继征（1982—），女，硕士，高级农艺师，研究方向：兰科植物种质创新与新品种选育。

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范继征（1982—），女，硕士，高级农艺师，研究方向：兰科植物种质创新与新品种选育。

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