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Comprehensive dna barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae)

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Insect Science 2024年第2期31卷 613-632页

作者： Yan Lai Kaiyu Li Xingyue Liu Deparment of Entomology Cllege of Plant ProtectionChina Agricultural UniversityBejingChina College of Bioogical Sciencs China Agricultural UniversityBeijingChina

Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae.Currently,the taxonomy of Chrysopidae lacks a comprehensive revision,which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents.We have established a dna barcode reference library of the Chinese green lacewings based on an approximately complete sampling(95.63%)in 25 of the 34 provincial regions in China,comprising 1119 barcodes of 25 genera and 197 species(representing 85%genera and 43.62%species from China).Combining other 1049 high quality green lacewing dna barcodes,we first inferred the optimal threshold of interspecific genetic divergence(1.87%)for successful species identification in multiple simulated scenarios based on present data.We further inferred the threshold of genetic divergence(7.77%)among genera with biocontrol significance.The inference and performance of the threshold appears to be mainly associated with the completeness of sampling,the proportion of closely related species,and the analytical approaches.Six new combinations,Apertochrysa platypa(Yang&Yang,1991)comb.nov.,Apertochrysa shennongana(Yang&Wang,1990)comb.nov.,Apertochrysa pictifacialis(Yang,1988)comb.nov.,Apertochrysa helana(Yang,1993)comb.nov.,Plesiochrysa rosulata(Yang&Yang,2002)comb.nov.,and Signochrysa hainana(Yang&Yang,1991),are proposed according to integrative species delimitation.Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings.Our study also provides a methodological reference in molecular delimitation of other insects.

关键词： Chrysopidae dna barcode genetic distance optimal threshold species delimitation

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dna barcoding of Pedicularis L.(Orobanchaceae):Evaluating four universal barcode loci in a large and hemiparasitic genus

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Journal of Systematics and Evolution 2011年第5期49卷 425-437页

作者： Richard H.REE Department of Botany Field Museum of Natural History

One application of dna barcoding is species identification based on sequences of a short and standardized dna region.In plants,various dna regions,alone or in combination,have been proposed and investigated,but consensus on a universal plant barcode remains elusive.In this study,we tested the utility of four candidate barcoding regions(rbcL,matK,trnH-psbA,and internal transcribed spacer(ITS)) as dna barcodes for discriminating species in a large and hemiparasitic genus Pedicularis(Orobanchaceae).Amplification and sequencing was successful using single primer pairs for rbcL,trnH-psbA,and ITS,whereas two primer pairs were required for matK.Patterns of sequence divergence commonly showed a "barcoding gap",that is,a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species,respectively.Considering primer universality,ease of amplification and sequencing,and performance in discriminating species,we found the most effective single-region barcode for Pedicularis to be ITS,and the most effective two-region barcode to be rbcL + ITS.Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample,and were effective in placing unidentified samples in known species groups.Our results suggest that dna barcoding has the potential to aid taxonomic research in Pedicularis,a species-rich cosmopolitan clade much in need of revision,as well as ecological studies in its center of diversity,the Hengduan Mountains region of China.

关键词： dna barcode Hengduan Mountains region ITS Pedicularis rbcL species identification.

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dna barcode Screening and Preliminary Study on Phylogeny of Sea Snake Based on Genes COI and cytb

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Agricultural Biotechnology 2021年第6期10卷 35-45页

作者： Xiangjun WANG Wen CHEN Haiying SU Provincial Key Laboratory of Amphibian and Reptile Research School of Life Science and EcologyHainan Tropic Ocean UniversitySanya 572022China Nanjing Normal University School of Life SciencesNanjing201146China School of Ocean Science and Technology Hainan Tropic Ocean UniversitySanya 572022China

[Objectives]The most common gene fragment used in animal dna barcode technology is COI,but it is not necessarily suitable for all species.This study was conducted to screen genes suitable for the dna barcode of sea snakes.[Methods]All COI and cytb gene sequences on GenBank were searched and downloaded.After the comparison with Mega software,clustering trees of MrBayes system were established.[Results]Interspecies distances were greater than intraspecies distances for the two genes.The topological structures of their molecular hierarchical clustering trees were clear,and the support rates were high.[Conclusions]Therefore,it is concluded that not the dna barcode of each species must be gene COI.Cytb is more suitable in terms of the mitochondrial gene of sea snakes.

关键词： Sea snake dna barcode Clustering tree COI gene cytb gene

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基于形态学与dna barcode技术探究芍药品种分类

基于形态学与DNA barcode技术探究芍药品种分类

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作者：李倩山东农业大学

学位级别：硕士

芍药(Paeonia lactiflora Pall.)是我国传统名花和药用植物,具有悠久的栽培和观赏历史,其应用形式多样,用作切花时深受市场欢迎,具有大量的市场需求和广阔的发展前景。本研究根据芍药切花的生产标准从国内主栽品种中初选65个芍药品种和... 详细信息

芍药(Paeonia lactiflora Pall.)是我国传统名花和药用植物,具有悠久的栽培和观赏历史,其应用形式多样,用作切花时深受市场欢迎,具有大量的市场需求和广阔的发展前景。本研究根据芍药切花的生产标准从国内主栽品种中初选65个芍药品种和野生种进行引种栽植,并复选出22个芍药切花的育种材料。对初选材料进行以形态学调查为依据的种源划分和分类检索表的制定;对复选材料进行以dna barcode技术为依托的亲缘关系的探究。本实验旨在探究芍药品种的分类和芍药切花育种材料间的亲缘关系,为芍药杂交过程中亲本选配提供理论基础。本实验的主要研究成果如下:1.以叶缘骨刺作为种特征的分类依据。根据叶片边缘有白色透明骨质细齿,引种材料均被鉴定为芍药(P.lactiflora)种下的栽培品种。2.以心皮特征作为芍药品种群种源划分的依据。根据心皮是否被毛,将26个芍药品种划分为原种芍药品种群(Subgroup of P.lactiflora),36个芍药品种分为毛果芍药品种群(subgroup of P.lactiflora.***.trichocarpa),在调查过程中,发现3个芍药品种的心皮高度瓣化,将此类品种归为芍药心皮瓣化品种群(subgroup of cultivars with carpel petaloid)。3.根据心皮特征、花型、花色等性状编制分类检索表。对泰安、济南、菏泽三地的供试芍药品种进行连续三年的性状调查,包括:心皮特征、花型、花色等。依据性状调查编制芍药品种的等距分类检索表,方便芍药品种的辨识,对芍药品种分类、园林应用和新品种的审定等方面具有一定的参考价值。4.dna barcode技术对芍药品种的鉴定。选择ITS2和psbA-trnH进行芍药品种间的鉴定。综合PCR扩增效率、测序质量、Blast和系统进化树的鉴定结果,选择ITS2作为芍药品种间鉴别的dna条形码。5.形态学分类与系统进化树分类的比较。复选芍药品种在形态学分类和ITS2进化分类中存在异同。每个种群内的大部分品种在进化树中的亲缘关系近,且三个种群内的大部分品种与芍药野生种的亲缘关系近,但不同种群内的部分品种间的亲缘关系存在交集,表明了单一分类方法存在的局限性,也表明形态分类中的芍药原种品种群和毛果芍药品种群的亲本来源可能存在过渡与交叉。

关键词：芍药毛果芍药心皮特征分类检索表 dna barcode ITS2 psbA-trnH

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樟科植物dna barcode及香樟系统地理学的初步研究

樟科植物DNA Barcode及香樟系统地理学的初步研究

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作者：高大伟华东师范大学

学位级别：硕士

dna barcode是指基于一小段dna序列来区分物种的方法。其准确、快速的特点在识别已知物种、发现新物种以及生物多样性研究方面都有着广阔的应用前景。在动物中,线粒体基因的细胞色素C氧化酶I号基因(COI)中一段长为约600bp的区间已经被... 详细信息

dna barcode是指基于一小段dna序列来区分物种的方法。其准确、快速的特点在识别已知物种、发现新物种以及生物多样性研究方面都有着广阔的应用前景。在动物中,线粒体基因的细胞色素C氧化酶I号基因(COI)中一段长为约600bp的区间已经被证实为适合大多数动物的dna barcode区间。但在植物中,由于植物自身的特点,dna barcode相对于其在动物中的研究来说要困难得多,并且至今还没有达成一致性观点。在陆生植物中,叶绿体中psbA-trnH基因间隔区间和一部分matK基因被认为是两个理想的但又饱受争议的dna barcode区间。本研究分析并比较了上述两区间在樟科7个属,共34个物种(包括许多亲缘关系很近的物种)中的区分效果,并通过香樟叶绿体基因组psbA-trnH和trnS-trnG基因间隔区间的测序,对其进行了系统地理学研究。结果表明:(1)psbA-trnH和matK区间的引物在所有34个樟科物种中的PCR扩增成功率都达到了100%。在34个物种中(包括许多近缘物种),psbA-trnH序列区分出了26个截然不同的序列,matK序列共区分出了22个不同的序列,分别占到了总数的76.47%和64.71%。两个区间在不同属物种之间都能够很好的区分,但在一些亲缘关系十分近物种的区分上还存在困难。另外将psbA-trnH以及matK序列组合起来,也没有显示出比单独的psbA-trnH区间能区分出更多的序列。(2)由于psbA-trnH区间在近缘物种之间的序列分化值(2.45%)要远远大于matK区间(0.36%),前者将近为后者的7倍,因此我们建议相比matK基因区间而言,叶绿体psbA-trnH区间作为陆生植物的首选质体dna barcode区间更合理。(3)另外运用实验所获得的樟科植物dna barcode数据,我们发现在NCBI数据库中香樟(Cinnamomum camphora)所对应的编号为AB331294的序列与本实验中获得的香樟该段区间所对应的序列两者之间有13个碱基的差别,序列分化大小达到了2.6%;而与本实验所获得的银木(Cinnamomum septentrionale)—香樟的一近缘种所对应的序列两者之间只有1个碱基的差别,序列分化只有0.3%,因此,我们认为NCBI数据库中编号为AB331294的序列并非对应的是香樟物种,而很可能是银木或者为银木的一个种内变异。(4)中国大陆香樟的遗传多样性非常低。

关键词： dna barcode psbA-trnH matK 樟科植物系统地理学香樟

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dna barcode:an effective tool for species identification of lepidopteran oak pests

DNA barcode:an effective tool for species identification of ...

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中国蚕学会2021年学术年会

作者： Ni Mingyang Gu Yujian Jiang Yiren Shi Shenglin Yang Ruisheng Department of Sericulture College of Bioscience and BiotechnologyShenyang Agricultural University

To improve the efficiency and accuracy of early forecast of Lepidopteran oak-infesting pests,dna barcode technique was established for quick species identification using mitochondrial cytochrome C oxidase subunit I（CO I） as the standard gene.This technique was used to amplify and sequence genomic dna samples from eggs and pupae of 11 species of Lepidopteran pests collected from oak.The dna barcoding standard genes of 594-708 bp were determined from eggs and pupae of Lepidopteran insects.There were differences of 0-2 bases in dna barcode sequences between conspecific eggs and pupae,with the sequence identity of 99.7%-100%.The average content of A,T,G and C of dna barcode sequences from Lepidopteran insects were 30.7%,38.5%,14.9% and 15.9%,respectively.The obtained dna barcode sequences had 91.4%-100% identity and 0-8.6% difference degree with GenBank-deposited dna barcode sequences from organisms of the genetically-closest relationship.Among them,dna barcode sequences from egg and pupa samples of 10 Lepidopteran insects had 99%-100% identity and 0-1.0% difference degree with homologous sequences in GenBank database,while the remaining samples had high difference degree（8.6%） with homologous sequences.The established dna barcoding technique is an effective tool for species identification of Lepidopteran pests using genomic dna from eggs and pupae of Lepidopteran insects.

关键词： dna barcode Oak pest Lepidopteran insects Molecular identification Cytochrome C oxidase subunit I

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barcodeFinder: An Integrated Tool for Discovering Novel dna barcode Efficiently

BarcodeFinder: An Integrated Tool for Discovering Novel DNA ...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Ping Wu University of Chinese Academy of Sciences State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of Sciences

dna barcode has been widely used for species identification and classification.Although standard barcodes for land plants were proposed,such as matK,rbcL and trnH-psbA,they generally presents inadequate resolution in lower taxonomic rank or specific taxa.Currently,the explosion of sequencing data offers abundant possibilities to uncover extra dna barcodes,yet it was hindered by the complexity of traditional practice of screening candidate barcodes as well as the lack of automatic tools.Here we developed barcodeFinder,an all-in-one pipeline which integrated data collecting and filtering,sequence variance evaluating and primer designing functions to accelerate the development of novel dna barcodes.With the assistance,we successfully found thirteen hyper-variant regions on chloroplast genome for Asteraceae suitable to be dna barcode.Plus,validated（in silico and in vitro） pairs of universal primers for amplification were also generated.

关键词： barcodeFinder dna barcode universal primer land plants

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Medaeops Guinot,1967(Brachyura,Xanthidae)from China seas,with the resurrection of Medaeops japonicus(Rathbun,1898)

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Journal of Oceanology and Limnology 2023年第6期41卷 2403-2417页

作者： Ziming YUAN Wei JIANG Zhongli SHA Laboratory of Marine Organism Taxonomy and Phylogeny Qingdao Key Laboratory of Marine Biodiversity and ConservationInstitute of OceanologyChinese Academy of SciencesQingdao 266071China Shandong Province Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of SciencesQingdao 266071China Laoshan Laboratory Qingdao 266237China University of Chinese Academy of Sciences Beijing 100049China

The xanthid genus Medaeops Guinot,1967 currently contains seven species reported from the Indo-West Pacific region.However,only one species,Medaeops granulosus(Haswell,1882),has been recorded from China seas and was once thought to be widespread in the Indo-West Pacific region.In this study,two species of the Medaeops granulosus species-group were identified during the analysis on Medaeops crabs from China seas.Medaeops japonicus(Rathbun,1898),which had previously been considered a junior synonym of M.granulosus,is shown to be a distinct species that can be distinguished from M.granulosus by the lower first anterolateral tooth,the larger and concentrated granules on carapace dorsally,and the different shape of the male’s first gonopod.In addition,a new recorded species,Medaeops edwardsi Guinot,1967,was reported from China seas for the first time.A molecular analysis was conducted to determine the status of each species,and an updated key for species of the genus Medaeops was provided.

关键词： euxanthine Xanthoidea crab Decapoda dna barcode

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ITS1:A dna barcode Better Than ITS2 in Eukaryotes?

ITS1:A DNA Barcode Better Than ITS2 in Eukaryotes?

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第十四届全国中药和天然药物学术研讨会

作者： Xin-Cun Wang Chang Liur Liang Huang Johan Bengtsson-Palme Haimei Chen Jian-Hui Zhang Dayong Cai Jian-Qin Li Chinese Academy of Medical Science University of Gothenburg

dna barcode is a short piece of dna sequence used for species determination and discovery.The internal transcribed spacer（ITS/ITS2） region has been proposed as the standard dna barcode for fungi and seed plants,and has been widely used in dna barcoding analyses for other biological groups,e.***.algae,protists,and animals.The ITS region consists of both ITS1 and ITS2 regions;here,a large scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects:PCR amplification,dna sequencing and species discrimination,in terms of the presence of dna barcoding gaps,species discrimination efficiency,sequence length distribution,GC content distribution and primer universality.In total,85,345 sequence pairs in ten major groups of eukaryotes,including ascomycetes,basidiomycetes,liverworts,mosses,ferns,gymnosperms,monocotyledons,eudicotyledons,insects,and fishes,covering611 families,3,694 genera,and 19,060 species,were analyzed.Using similarity-based methods,we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups,families,and genera.Using Fisher’s exact test,we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera,which are most sample-rich or representative.By in silico PCR amplification evaluation,primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers.Additionally,shorter length of amplification product and lower GC content were discovered to be two other advantages of ITS1 for sequencing.In summary,ITS1 represents a better dna barcode than ITS2 for eukaryotic species in most situations.

关键词： dna barcode internal transcribed spacer 1 internal transcribed spacer 2,meta-analysis species identification

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dna barcoding for the identification of Limonia crane flies(Diptera:Limoniidae)from China,including a new species and a newly recorded species

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动物分类学报:英文版 2023年第3期48卷 236-248页

作者： Hanhuiying Lü Yaru Chen Jinlong Ren Ning Wang Ding Yang Xiao Zhang Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management College of Plant Health and Medicine/College of Grassland ScienceQingdao Agricultural UniversityQingdao 266109China Key Laboratory of Biohazard Monitoring and Green Prevention and Control in Artificial Grassland Ministry of Agriculture and Rural AffairsInstitute of Grassland ResearchChinese Academy of Agricultural SciencesHohhot 010010China Key Laboratory of the Pest Monitoring and Safety Control on the Crop and Forest College of AgronomyXinjiang Agricultural UniversityUrumqi 830052China College of Plant Protection China Agricultural UniversityBeijing 100193China

The genus Limonia Meigen,1803 is globally distributed with 216 known species/subspecies,of which 30 are recorded from China.In this study,we firstly use dna barcodes(mt COI)to identify specimens of Limonia from China,result in a discovery of three species.Considering the morphological data,these species were identified as L.albiterminalis Lü,Ren&Zhang,sp.nov.,L.juvenca Alexander,1935(new record in China),and L.macrostigma(Schummel,1829),respectively.Six COI sequences of the three species were provided,analyzed with other 24 COI sequences from Limonia species.The result indicates that intraspecific distances in the genus are generally less than 2.2%,interspecific distances range from 7.9%to 17.2%,and there is no overlap between intra-and interspecific distances.Redescription and illustrations of L.juvenca and illustration of male hypopygium of L.macrostigma,as well as the key to the Chinese Limonia crane flies,are all provided.

关键词： dna barcode taxonomy Chinese fauna COI Limoniinae

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