DNA条形码及其在海洋浮游动物生态学研究中的应用

浮游动物的准确鉴定是浮游动物生态学研究的基础.传统的基于形态特征的鉴定不仅费时费力,而且部分类群特别是浮游幼体由于形态差异细微,鉴定存在困难,导致物种多样性被低估.DNA条形码(DNA barcodes)技术为浮游动物物种鉴定提供了一个有力工具,已迅速应用于海洋浮游动物生态学研究.本文介绍了DNA条形码的基本概念、优势及局限性,总结了该技术(主要是基于线粒体细胞色素C氧化酶第一亚基(mtCOI)基因序列片段的DNA条形码)在海洋浮游动物物种快速鉴定、隐种发现、营养关系研究、生物入侵种监测、群落历史演变反演、种群遗传学以及生物地理学中的成功应用.随着DNA条形码数据库信息量覆盖率的不断提高和新一代测序技术的快速发展,DNA条形码将提供除了种类鉴定外更加丰富的信息,从而帮助人们更好地理解海洋浮游动物的多样性及其在生态系统中的功能,推动海洋浮游动物生态学的发展.     

药用植物DNA条形码鉴定研究进展

DNA条形码是利用相对较短的标准DNA片段对物种进行快速准确鉴定的一门技术。DNA条形码技术可以从分子水平弥补传统鉴定方法的一些不足。该技术具有良好的通用性,使得物种鉴定过程更加快速,已经广泛应用于动物物种的鉴定研究中。近年来,随着药用植物DNA条形码鉴定研究的快速发展,逐渐形成了药用植物和植物源中药材鉴定的完善体系。本文综述了DNA条形码技术鉴定药用植物的原理,介绍了中草药传统鉴定方法及其缺陷、使用DNA条形码技术鉴定植物源药材的意义以及DNA条形码在药用植物鉴定中的应用,对其应用前景进行了展望。     

DNA条形码技术的研究进展及其应用

DNA条形码技术(DNA Barcod ing)是通过对一个标准目的基因的DNA序列进行分析从而进行物种鉴定的技术。这个概念的原理与零售业中对商品进行辨认的商品条形码是一样的。简单地说,DNA条形码技术的关键就是对一个或一些相关基因进行大范围的扫描,进而来鉴定某个未知的物种或者发现新种[1—3]。自从提出DNA条形码的概念以来,这种新兴分类学技术已经引起了越来越多的生物学家的关注。DNA条形码技术是分类学中辅助物种鉴定的新技术,它代表了生物分类学研究的一个新方向[4],因此它在生态、环境、食品等诸多领域都将会有广泛的应用[5]。本文概括综述了DNA条形码技术的发展历史、原理与操作,分析了其在生物分类中的应用及应用上的优势与限制,对DNA条形码技术在鱼类学研究的意义与可行性进行了探讨。1 DNA条形码技术的发展历史2003年,Herbert研究发现利用线粒体细胞色素C氧化酶亚基Ⅰ(M itochondrial cytochrom ecoxidase subun itⅠ,COⅠ)基因一段长度为648bp的片段,能够在DNA水平上成功的区分物种,并且认为利用COⅠ基因从分子演化的角度,将提供一种快速、简便、可信的分...     

基因组学技术在生物多样性保护研究中的应用

在分子生物学、细胞生物学、微生物学、遗传学等学科的推动下, 生物多样性研究从仅关注宏观表型的博物学, 迅速演化为涵盖生态系统、物种和遗传多样性等多个维度的综合性生命科学。组学技术, 尤其是DNA测序技术的更新和发展, 使获取DNA序列所需的成本大幅下降, 促进了近年来其在生物多样性研究中取得的一系列令人瞩目成就。本文将从物种水平的遗传多样性和群落水平的物种多样性两个层面总结和介绍与DNA相关的组学技术在生物多样性研究中的一些创新和应用。其中, 物种水平主要是总结单一个体的基因组和单物种多个体在时空多个维度上的群体遗传研究; 而群落水平的物种多样性层面主要总结现有的分子鉴定技术(metabarcoding, eDNA, iDNA等), 以及上述新技术在群落多样性评估、旗舰保护物种监测以及物种间相互作用关系等研究中的应用。     

DNA条形码及其在生物多样性研究中的应用

DNA条形码是利用生物体内标准的、有足够变异的、易扩增且相对较短的DNA片段对物种进行快速准确鉴定的技术。自2003年DNA条形码相关概念提出以来广受关注,国内外相继开展了DNA条形码及信息系统建设研究,为DNA条形码技术的发展提供了坚实的研究基础和生物信息学分析平台。DNA条形码技术弥补了传统分类学的不足,为生物多样性研究提供了新的思路和方法。本文介绍了DNA条形码的产生与发展过程,国内外DNA条形码技术与信息系统建设研究进展,重点阐述了DNA条形码技术在物种鉴定、濒危物种保护、隐存种发现、生物多样性评估等研究领域中的应用。最后结合DNA条形码技术目前存在的问题,对其在相关研究领域的应用前景进行了展望。     

动物DNA条形码之分析方法研究进展

DNA条形码是一段可用于物种鉴定的DNA序列。本文综述了近年来多种基于DNA条形码的分析方法及其在物种鉴定和隐存种发现中的应用,主要包括遗传距离法、进化树法、相似性比对法、诊断法和统计分类法等,旨在为这一技术的广泛应用提供参考。     

DNA条形码在生态学研究中的应用与展望

DNA条形码是利用标准的DNA片段对物种进行快速鉴定的技术,已在生物学各相关领域得到广泛应用。随着DNA条形码技术的不断发展和完善,已成功应用于生态学领域的相关研究中。本文综述了DNA条形码在物种快速鉴定和隐存种发现、群落系统发育重建和生态取证、群落内物种间相互关系研究等方面的应用,并介绍了DNAmetabarcoding技术和环境DNA条形码在生物多样性和生态学研究领域中的应用。最后,结合新的测序技术和未来大科学装置的发展,在相关数据库逐渐完善,新分析方法和计算模型不断开发使用的情景下,对DNA条形码在生态学相关领域的应用前景进行了展望。     

植物DNA条形码在系统发育研究中的应用

<正>1常用植物DNA条形码物种的准确鉴定是开展科学研究和生物多样性保护的先决条件,但根据形态学特征进行物种鉴定对非专业人员而言比较困难。即使是专业人员,面对纷繁复杂的物种,要想逐一鉴定也难以实现。DNA条形码技术(DNA barcoding)为物种的快速、准确鉴定提供了可能(Hebert et al.,2003)。线粒体COI基因作为动物的DNA条形码已得到广泛应用。但对     

DNA条形码技术在常见水生动物分类中的应用

DNA条形码(DNA barcoding)技术是逐渐发展起来的新兴分子技术,它通过利用生物体内一段特异的DNA序列快速而精确进行物种识别。DNA条形码技术不仅可以用于物种的鉴定和分类,同时也帮助生物学家深入了解物种之间的亲缘关系以及生态系统内的相互作用,提供了一种迅速而有效的分类学方法来细化分类学上现存的标准,因而成为分类学领域的前沿技术。本文概述了DNA条形码技术在部分水生物种中的广泛应用以及对未来的展望。     

DNA条形码：物种分类和鉴定技术

当前,一项称为“生命的条形码”计划正在欧美等国展开,其目的是实现对地球上现存的约1000万物种进行快速和准确的鉴定。DNA条形码是一种利用短的DNA序列对物种进行鉴定的技术。对DNA条形码的概念和原理进行了介绍,举例说明了其在物种分类、遗传多样性及物种鉴定研究中广泛的利用价值,阐述了当前该领域的研究现状,对未来的发展方向进行了展望。     

A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators

Accurate identification of species that are consumed by vertebrate predators is necessary for understanding marine food webs. Morphological methods for identifying prey components after consumption often fail to make accurate identifications of invertebrates because prey morphology becomes damaged during capture, ingestion and digestion. Another disadvantage of morphological methods for prey identification is that they often involve sampling procedures that are disruptive for the predator, such as stomach flushing or lethal collection. We have developed a DNA-based method for identifying species of krill (Crustacea: Malacostraca), an enormously abundant group of invertebrates that are directly consumed by many groups of marine vertebrates. The DNA-based approach allows identification of krill species present in samples of vertebrate stomach contents, vomit, and, more importantly, faeces. Utilizing samples of faeces from vertebrate predators minimizes the impact of dietary studies on the subject animals. We demonstrate our method first on samples of Adelie penguin (Pygoscelis adeliae) stomach contents, where DNA-based species identification can be confirmed by prey morphology. We then apply the method to faeces of Adelie penguins and to faeces of the endangered pygmy blue whale (Balaenoptera musculus brevicauda). In each of these cases, krill species consumed by the predators could be identified from their DNA present in faeces or stomach contents.     

DNA-based methods for monitoring invasive species: a review and prospectus

The recent explosion of interest in DNA-based tools for species identification has prompted widespread speculation on the future availability of inexpensive, rapid, and accurate means of identifying specimens and assessing biodiversity. One applied field that may benefit dramatically from the development of such technologies is the detection, identification, and monitoring of invasive species. Recent studies have demonstrated the feasibility of DNA-based tools for such important tasks as confirmation of specimen identity and targeted screening for known or anticipated invaders. However, significant technological hurdles must be overcome before more ambitious applications, including estimation of propagule pressure and comprehensive surveys of complex environmental samples, are to be realized. Here we review existing methods, examine the technical difficulties associated with development of more sophisticated tools, and consider the potential utility of these DNA-based technologies for various applications relevant to invasive species monitoring.     

Systematics of malaria vectors with particular reference to the Anopheles punctulatus group

The appearance of groups and complexes of closely related cryptic or sibling species in many of the anopheline taxa has impeded studies on malaria transmission and the evaluation of control strategies which have relied on morphological characters to identify the vector species involved. The advantages of morphological identification are low cost, speed and simplicity, which allow large numbers of specimens to be processed rapidly in the field. The need for accurate identification is crucial, as time and money may be wasted in studying and controlling species of no medical importance. Various techniques such as cross-mating, chromosome studies and allozyme analysis have been developed to resolve problems of identifying sibling species, though none, as yet, can match the speed and simplicity afforded by morphology markers. The latest of these identification methods comes from advances that have been made in DNA-based technology. Although costly and requiring fairly sophisticated laboratory support, methods such as DNA probe hybridisation and PCR are the quickest and most user-friendly to date. The use of DNA has other advantages in the study of intraspecific differences and in providing characters for phylogenetic studies. This review looks at the development of DNA-based techniques for taxonomic and systematic studies of anopheline mosquitoes. The Anopheles punctulatus group of the southwest Pacific is featured as an example of how this technology has been applied and how it has progressed.     

Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species

Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.     

Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis

Phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genus Xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 new Xanthomonas-specific molecular markers, within loci coding for Xanthomonas-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-Xanthomonas species, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15 Xanthomonas spp. suggested species-specific hybridization patterns, which allowed discrimination among the different Xanthomonas species. Having in mind that DNA-based methods of diagnosis are particularly hampered for unsequenced species, namely, Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans, for which comparative genomics tools to search for DNA signatures are not yet applicable, emphasis was given to the selection of informative markers able to identify X. fragariae, X. axonopodis pv. phaseoli, and X. fuscans subsp. fuscans strains. In order to avoid inconsistencies due to operator-dependent interpretation of dot blot data, an image-processing algorithm was developed to analyze automatically the dot blot patterns. Ultimately, the proposed markers and the dot blot platform, coupled with automatic data analyses, have the potential to foster a thorough monitoring of phytopathogenic xanthomonads.     

Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

Background  

The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification.     

Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?

Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through rapid DNA-based tests. The question of whether we can reliably detect and identify species of Aspergillus and Penicillium turns mainly upon the completeness of our alpha taxonomy, our species concepts, and how well the available DNA data coincide with the taxonomic diversity in the family Trichocomaceae. No single gene is yet known that is invariant within species and variable between species as would be optimal for the barcode approach. Data are published that would make an MLST approach to isolate identification possible in the most well-studied clades of Aspergillus and Penicillium.     

Birdstrikes and barcoding: can DNA methods help make the airways safer?

While flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochrome c oxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA-based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.     

Inferring species membership using DNA sequences with back-propagation neural networks

DNA barcoding as a method for species identification is rapidly increasing in popularity. However, there are still relatively few rigorous methodological tests of DNA barcoding. Current distance-based methods are frequently criticized for treating the nearest neighbor as the closest relative via a raw similarity score, lacking an objective set of criteria to delineate taxa, or for being incongruent with classical character-based taxonomy. Here, we propose an artificial intelligence-based approach - inferring species membership via DNA barcoding with back-propagation neural networks (named BP-based species identification) - as a new advance to the spectrum of available methods. We demonstrate the value of this approach with simulated data sets representing different levels of sequence variation under coalescent simulations with various evolutionary models, as well as with two empirical data sets of COI sequences from East Asian ground beetles (Carabidae) and Costa Rican skipper butterflies. With a 630-to 690-bp fragment of the COI gene, we identified 97.50% of 80 unknown sequences of ground beetles, 95.63%, 96.10%, and 100% of 275, 205, and 9 unknown sequences of the neotropical skipper butterfly to their correct species, respectively. Our simulation studies indicate that the success rates of species identification depend on the divergence of sequences, the length of sequences, and the number of reference sequences. Particularly in cases involving incomplete lineage sorting, this new BP-based method appears to be superior to commonly used methods for DNA-based species identification.     

Yeast species recognition from gene sequence analyses and other molecular methods

This review discusses DNA-based methods used for identification of yeasts. Nuclear DNA reassociation was the first quantitative molecular method employed for recognition of yeast species and has provided a baseline for interpretation of other molecular comparisons. Among these, gene sequencing is the most definitive method, with ribosomal RNA gene sequences providing the preponderance of available data. Multigene analyses that include the sequences of protein encoding genes are being increasingly developed to provide a more definitive resolution of species. A number of rapid identification methods, such as denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), and flow cytometry, which are based on species-specific gene sequences, are available for use in diagnostic laboratories.