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基于线粒体COⅠ基因的齿小蠹属昆虫DNA条形码研究 总被引:2,自引:0,他引:2
齿小蠹属(鞘翅目: 小蠹科)昆虫是植物检疫中经常截获的类群, 为探讨线粒体细胞色素C氧化酶亚基Ⅰ(COⅠ)基因的特定区段作为DNA条形码快速准确鉴定齿小蠹种类的可行性, 以齿小蠹属昆虫为研究对象, 测定分析了线粒体COⅠ基因462 bp碱基序列。序列分析结果显示: 变异位点为259个, 保守位点203个, 简约信息位点181个, 自裔位点78个。所有位点中, A, G, C和T碱基平均含量分别为30.7%, 16.5%, 17.0%和35.8%。A+T含量较高, 为66.5%, 明显高于G+C含量, 表现明显的A+T碱基偏嗜, 且A与T含量相当, 符合昆虫线粒体基因碱基组成的基本特征。转换与颠换结果显示: 该段序列未达到饱和, 可以得到准确的进化分析。利用Kimura 2-parameter模型分析遗传距离得到, 同物种间的遗传距离介于0.002~0.007之间, 不同种间的遗传距离介于0.056~0.431间, 平均遗传距离为0.199, 说明该段序列能够区分不同物种。基于COⅠ基因序列构建的邻接法系统发育树(NJ树)显示, 同一物种聚为同一小支, 且分支自展值均为100%; 近缘种能聚集在一起, 且置信度很高(≥97%)。结果表明应用基于COⅠ基因片段的DNA条形码进行齿小蠹属昆虫分类鉴定具有可行性。 相似文献
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《昆虫知识》2013,(1)
对嗡蜣螂属Onthophagus 12种蜣螂的线粒体COⅠ基因3'端部分序列(731 bp)进行了比较,结果显示,COⅠ序列的变异位点213个,简约信息位点167个。碱基替代主要发生在第3位点(64次),占替代总数的83.12%。除掘嗡蜣螂O.fodiens与婪嗡蜣螂O.lenzi小于2%外,其余种间遗传距离在8.1%15.8%之间,种内遗传距离为015.8%之间,种内遗传距离为00.2%。单倍型多样性(Hd)和核苷酸序列多样性(Pi)分别为0.944±0.030和0.10518±0.0045。滑动窗口分析表明,可变位点频率在2400.2%。单倍型多样性(Hd)和核苷酸序列多样性(Pi)分别为0.944±0.030和0.10518±0.0045。滑动窗口分析表明,可变位点频率在240290 bp、675 bp附近较高。NJ树聚类结果与传统形态学分类相吻合:外群代表种分化最早,种间聚成一分支,种内个体优先聚集种下。本文认为COⅠ基因适合作为嗡蜣螂属物种鉴定的DNA条形码。 相似文献
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基于线粒体COⅠ基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究 总被引:1,自引:0,他引:1
选择线粒体COⅠ基因作为分子标记,进行沙鳅亚科鱼类(Botiinae)DNA条形码及其分子系统发育研究。研究获得了沙鳅亚科7属19种共131个个体的COⅠ基因序列,利用MEGA5.0软件分析了沙鳅亚科鱼类COⅠ基因的序列特征,计算了种内及种间遗传距离。沙鳅亚科鱼类的分子系统发育关系的重建分别采用NJ法和Bayesian法。研究发现,沙鳅亚科COⅠ基因的碱基组成为: A 24.4%、T 29.5%、G 18.0%、C 28.1%。沙鳅亚科鱼类种内平均遗传距离为0.0020.000,种间平均遗传距离为0.1480.008。DNA条形码研究结果显示,所分析的19种沙鳅鱼类各自分别聚成单系分支,表明COⅠ基因在本研究中具有100%的物种鉴别率。同时,系统发育分析支持各属的单系性,并且结果显示沙鳅亚科鱼类聚为两个分支,其中一支由薄鳅属和副沙鳅属构成,另一分支则包括: (沙鳅属、色鳅属)和 中华沙鳅属、(缨须鳅属、安彦鳅属)。因此,COⅠ基因可以作为有效的分子标记对沙鳅亚科进行DNA条形码研究以及分子系统发育研究。
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本文介绍了DNA条形码分析中常用的距离方法,包括简单的距离方法、基于阈值的距离方法和基于模糊成员关系的距离方法,并且以松毛虫属7个近缘种的COⅠ数据为例,运用基于阈值的距离方法进行演示分析。 相似文献
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《Journal of Asia》2023,26(4):102136
We monitored hitchhiker insect pests on vessels arriving to Korea from foreign countries. A survey of 416 foreign vessels was conducted from June 1, 2018 to October 29, 2019. A total of 1,141 hitchhiker insects were collected by interception or by hand. Individuals were identified to the species level whenever possible using DNA barcoding and morphological re-examination. Of the 1,141 hitchhikers, a total of 439 species from 81 families and 12 orders, including 54 species (93 individuals) not-distributed in Korea, were identified. Among the 93 individuals from the 54 species not distributed in Korea, 78 individuals were collected alive. In particular, three regulated species in Korea, Erthesina fullo (Pentatomidae, Hemiptera) (hitchhiking route: China > Yeosu, Korea), Tessaratoma papillosa (Tessaratomidae, Hemiptera) (China > Yeosu, Korea), Noctua pronuba (Noctuidae, Lepidoptera) (Singapore > Pohang, Korea) were detected, nine species, Dicranocephalus wallichii (Scarabaeidae, Coleoptera), Palpita quadristigmalis (Crambidae, Lepidoptera), Lymantria xylina (Erebidae, Lepidoptera), Odontopera aurata, Semiothisa cinerearia (Geometridae, Lepidoptera), Mythimna pallidicosta (Noctuidae, Lepidoptera), Euhampsonia serratifera (Notodontidae, Lepidoptera), Arippara disticha (Pyralidae, Lepidoptera), and Psilogramma lukhtanovi (Sphingidae, Lepidoptera) were discovered as multiple detection over years or months, and three species, Lemyra rhodophilodes (Erebidae, Lepidoptera), Malacosoma dentata (Lasiocampidae, Lepidoptera), and Chondracris rosea (Acrididae, Orthoptera) were multiple detected from single vessel. Therefore, we suggest that hitchhiker monitoring on vessels travelling along navigated routes should be conducted in addition to performing a risk assessment of hitchhiker insect pest species not distributed in Korea that includes regulated species. 相似文献
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DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity
Naro-Maciel E Reid B Fitzsimmons NN LE M Desalle R Amato G 《Molecular ecology resources》2010,10(2):252-263
DNA barcoding is a global initiative that provides a standardized and efficient tool to catalogue and inventory biodiversity, with significant conservation applications. Despite progress across taxonomic realms, globally threatened marine turtles remain underrepresented in this effort. To obtain DNA barcodes of marine turtles, we sequenced a segment of the cytochrome c oxidase subunit I (COI) gene from all seven species in the Atlantic and Pacific Ocean basins (815 bp; n = 80). To further investigate intraspecific variation, we sequenced green turtles (Chelonia mydas) from nine additional Atlantic/Mediterranean nesting areas (n = 164) and from the Eastern Pacific (n = 5). We established character-based DNA barcodes for each species using unique combinations of character states at 76 nucleotide positions. We found that no haplotypes were shared among species and the mean of interspecific variation ranged from 1.68% to 13.0%, and the mean of intraspecific variability was relatively low (0–0.90%). The Eastern Pacific green turtle sequence was identical to an Australian haplotype, suggesting that this marker is not appropriate for identifying these phenotypically distinguishable populations. Analysis of COI revealed a north–south gradient in green turtles of Western Atlantic/Mediterranean nesting areas, supporting a hypothesis of recent dispersal from near equatorial glacial refugia. DNA barcoding of marine turtles is a powerful tool for species identification and wildlife forensics, which also provides complementary data for conservation genetic research. 相似文献
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Trace Akankunda Hien To Carlos Rodriguez Lopez Remko Leijs Katja Hogendoorn 《Molecular ecology resources》2020,20(3):692-705
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost‐effective approach for targeting small sets of informative genes from multiple samples. In this context, high‐throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three‐step nested PCR approach targeting near full‐length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high‐throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol‐preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high‐quality multilocus barcodes from insect collections. 相似文献
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A synopsis of the P. amatista species-group in Colombia is provided. Five taxa are considered valid at species level, male and female phenotypes are associated, diagnosed and data on their distribution are given. The geographic variability of the species is discussed, and Penaincisalia celosia new species is described from specimens collected in an isolated branch of the central range in Colombian Andes. We present evidence to consider P. galeraensis (Salazar, Schmidt-Mumm, & Johnson) as a junior synonym of P. albalineata (Johnson). DNA barcodes provided additional information, which was in perfect agreement with the external characters in two of the five species. Interspecific distances were found to range from 0.6% to 6.6% (average 4.3), whilst their mean intraspecific variation ranges from 0.0% to 3.3% (average 0.7%). 相似文献
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线粒体是存在于绝大多数真核细胞内的一种基本的重要的细胞器,其具有相对独立的遗传系统。线粒体基因在真核生物具有高保守性,线粒体DNA(mtDNA)已被广泛应用于发病机理、临床诊断、遗传变异、生物进化等多方面的研究。1981年,Anderson用氯化铯密度梯度分离得到线粒体DNA(mtDNA),进行了全序列分析。此后,mtDNA的研究日益得到重视。已有的mtDNA提取方法概括起来可分为密度梯度离心法、酶消化法、柱层析法、氯化铯超速离心法、碱变性法和改进高盐沉淀法等,通过对以上方法的比较,发现改进高盐沉淀法具有简便、经济、易重复等优点。 相似文献
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Kun Luo ShiLin Chen KeLi Chen JingYuan Song Hui Yao Xinye Ma YingJie Zhu XiaoHui Pang Hua Yu XiWen Li Zhen Liu 《中国科学:生命科学英文版》2010,53(6):701-708
DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification. 相似文献
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Yunheng Ji Changkun Liu Zhenyan Yang Lifang Yang Zhengshan He Hengchang Wang Junbo Yang Tingshuang Yi 《Molecular ecology resources》2019,19(5):1333-1345
Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required. 相似文献
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Tingting Xie Michael C. Orr Dan Zhang Rafael R. Ferrari Yi Li Xiuwei Liu Zeqing Niu Mingqiang Wang Qingsong Zhou Jiasheng Hao Chaodong Zhu Douglas Chesters 《Molecular ecology resources》2023,23(7):1526-1539
The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach. 相似文献
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Wing Hing Wong Ywee Chieh Tay Jayanthi Puniamoorthy Michael Balke Peter S. Cranston Rudolf Meier 《Molecular ecology resources》2014,14(6):1271-1280
Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction (‘direct PCR’) and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands. 相似文献