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25 December 2012, Volume 34 Issue 6
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  • Articles
    WANG Hong-, WANG Yu-Hua-, YANG Zhu-Liang-, LI De-Zhu
    2012, 34(6):  1-3. 
    Abstract ( 1430 )   HTML ( )   PDF (279KB) ( 1655 )   Save
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    The Next-Generation Flora iFlora
    LI De-Zhu-, WANG Yu-Hua-, YI Ting-Shuang
    2012, 34(6):  525-531.  doi:10.3724SP.J.1143.2012.12135
    Abstract ( 2237 )   HTML ( )   PDF (764KB) ( 2774 )   Save
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     The 21st century has witnessed a rapid development in technologies of molecular biology and computer informatics. Fundamental changes have taken place in means and methods in which humans take cognition of the world. Based on the currently available eFlora and combining this with elements of nextgeneration sequencing techniques, DNA sequence data, geographical information system data and computer information technology, the next-generation Flora (iFlora) is bursting. Through a series of key technological innovations and integrations, the main objective of iFlora is to construct the next-generation Flora, which will fulfill the function of accurately and rapidly identifying species and acquiring speciesrelated digital information. iFlora will greatly advance the development of plant taxonomy, phylogenetics, evolutionary biology, ecology, biogeography, conservation biology and other related disciplines. Furthermore, iFlora will be a valuable tool for biodiversity conservation and sustainable utilization of biological resources, ecological security, public education and services, and will profoundly promote public understanding of biodiversity. The application of iFlora will tremendously nurture and boost the taxasphere and bioliterate world, and will be a new focal point that may reshape modern botany at the global and regional levels.

    The Development of Classical Plant Taxonomy and iFlora
    FANG Wei, LIU En-De
    2012, 34(6):  532-538.  doi:10.3724/SP.J.1143.2012.12144
    Abstract ( 2187 )   HTML ( )   PDF (744KB) ( 2979 )   Save
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    The paper briefly introduces four basic parts in classical plant taxonomy: identification, description, nomenclature and classification. First, identification: Interactive identification (like deltaintkey) is one mean of morphological identification; pattern recognition could be applied to photographic identification; the core of species identification is the molecular identification which reveals the hereditary essence of species. Second, description: DELTA System or analogous systems whose language is aligned with logical computer will be the basic language of the nextgeneration Flora (iFlora). Third, nomenclature: the last 20 years have witenessed some challenges and the desire for change of the ICBN (International Code of Botanical Nomenclature, which is now the International Code of Nomenclature for Algae, Fungi, and Plants). Two typical examples are the Draft BioCode and PhyloCode. The attempts will promote the change of nomenclatural rules, which likely to be reflected in iFlora. Fourth, classification: the molecular phylogenetic systems, represented by the APG System (progressing through APGI, II, and III), is becoming the dominant system of plant classification. However, at the species level, the genetic information cannot stand alone for the definition of a species. We need access to comprehensive information of characters, which will also promote the uniting of morphological traits, genetic traits, distribution data and other information. Familiarization with and mastering of these new techniques and ideas are essential. Undoubtedly, this integration will provide an important reference point for the design and compilation of the iFlora. In the coming decade, iFlora will be the embodiment of the achievements of modern plant taxonomy.

    The Potential Contribution of Plant DNA Barcoding and iFlora to Plant Germplasm Conservation
    YANG Xiang-Yun, CA Jie, ZHANG Ting, DU Yan
    2012, 34(6):  539-545.  doi:10.3724/SP.J.1143.2012.12149
    Abstract ( 2272 )   HTML ( )   PDF (741KB) ( 2319 )   Save
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    Plant diversity is the key element of ecosystem, and plays an important role in our daily life and socioeconomic prosperity. Preservation and utilization of plant diversity is the cornerstone of human welfare and civilization, and an essential strategy to address global climate change. Although the plant conservation activities have been achieved significantly in the past decades worldwide, there are gaps existent that may minimize the effort to fulfill the Global Strategy for Plant Conservation (2011-2020), e.g., the complexity of species origin and evolution, the lack of sufficient species information, and the shrunken taxonomy expertise. We account for the plant conservation achievement in China and point part of constrains for the success of China’s strategy for plant conservation, which could be removed with the conceiving and implementation of the nextgeneration Flora, or iFlora project. DNA barcoding is an important element of iFlora. We brief the application of plant DNA barcoding to accurately identify species in the bryophyte genus Herbertus and in a number of genera of seed plants, such as Ficus, Pedicularis, Tacca, Taxus and Trichoshanthes.

    Trends of iFlora by Literature and Information Analysis
    YANG Ya-, WANG Yu-Hua-, DU Ning- , WANG Chun-Ming
    2012, 34(6):  546-554.  doi:10.3724/SP.J.1143.2012.12142
    Abstract ( 2253 )   HTML ( )   PDF (2234KB) ( 1909 )   Save
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    Advances in networking and information technology are gradually changing our ways of learning, cognition and living. This paper employed the methods of bibliometry and retrieval to analyze research papers and information about DNA barcoding, biodiversity database, DNA sequencing technology and mobile identification devices which are related to iFlora research. The results indicate that: (1) The research field of plant DNA barcoding is expanding, but the exploration of a highresolution DNA barcode and combinations of barcodes is still on the top of the agenda. And integrated studies of plant taxonomy, plant systematics and evolution, ecology, plant diversity etc. are constantly developing; (2) The explosive growth of biodiversity information databases provides the foundation for the accumulation and expansion of knowledge about iFlora; (3) The thirdgeneration sequencing technology has emerged and rapidly developing. The miniaturization of sequencing equipment will soon become feasible; (4) Only a few experimental devices which can assist with the identification of plant species have appeared so far;(5)A cyberinfrastructure collaborative for the plant sciences promote interdisciplinary research and product development. Finally, the paper concludes with a discussion of the iFlora research plan and shows that it is an inevitable trend in future studies on plant diversity.

    A Proposed Framework for iFlora
    CENG Chun-Xia, YANG Jun-Bei, YANG Jing, YI Ting-Shuang, LIN Chun-Yan
    2012, 34(6):  555-561.  doi:10.3724/SP.J.1143.2012.12143
    Abstract ( 1802 )   HTML ( )   PDF (2929KB) ( 2060 )   Save
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    The nextgeneration Flora, or iFlora is an open application system (intelligent device) for plant species identification and data extraction. It derives from the accumulation of traditional plant taxonomy and related disciplines, but also integrates modern DNA sequencing technologies for collection and management of species information based on highspeed computer digitization, network technology and cloud computing analysis platform. Through twoway communication with this system, on one hand, new data and technology can be constantly integrated to enrich the content and function of the iFlora, on the other hand, to acquire the needed species information by means of variously identified pathways to achieve a rapid, accurate and convenient identification of species, so that it meets the cognitive demands of not only professional organizations but also the general public at different levels. The aim of this paper is to: 1) explain the construction of the iFlora application device, the component libraries (including information on voucher specimens, molecular materials and DNA sequences), and their importance; 2) point out the crucial role of digitizing species information and the open cloud computing service platform for data analysis because of the high integration and assembling capabilities of iFlora; and 3) discuss the challenges faced by the iFlora projects and outline possible intelligent device and application prospects in the near future.

    Some Considerations on Data Integration for the Next-Generation Flora (iFlora) and Flora Revision—— A Case Study of Gaultheria (Ericaceae)
    LU Lu-, WANG Hong-, LI De-Zhu
    2012, 34(6):  562-584.  doi:10.3724/SP.J.1143.2012.12145
    Abstract ( 2837 )   HTML ( )   PDF (13293KB) ( 2366 )   Save
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    The next-generation intelligent Flora (iFlora) is designed to integrate current botanical knowledge, with molecular biology information and computer technology. The most important and urgent task for iFlora development is to search for an approach to incorporate all useful data into an accurate, most up-to-date and complete information database for a taxon, and hierarchically classify these data to meet different demands from iFlora users, to provide the user an authentic, scientific researchbased platform for sharing botanic knowledge, and associated valuable information for the benefit of national economy and quality of our life. In this study, we summarized the innovations, hierarchical classifications and functions of data for iFlora, in contrast of that of the previous Floras and the frequentlyused digital plant databases or eFloras. The innovation and essential of data compilation and integration of the iFlora was emphasized as intelligent assembly of data from DNA barcodes, key morphological characters, digital images and molecular phylogenetics with the support of computer techniques to achieve intelligent plant identification. We attempted to integrate previously assembled research data into the iFlora, and list three hierarchically classified data and their functions, and related issues, with the genus Gaultheria and one of its species, G.hookeri, as test case.

    A Synopsis of Technical Notes on the Standards for Plant DNA Barcoding
    GAO Lian-MIng-, LIU Jie-, CAI Jie-, YANG Jun-Bo-, ZHANG Ting-, LI De-Zhu
    2012, 34(6):  592-606.  doi:10.3724/SP.J.1143.2012.12138
    Abstract ( 3490 )   HTML ( )   PDF (6225KB) ( 4507 )   Save
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    DNA barcoding is a technique using one or a few standardized DNA regions from different genomes for rapid species identification, which is used in the field of taxonomy, ecological surveys and assessment of biodiversity. Because of the plant natural particularity and the DNA barcodes used for plants differing from animals, the standards provided by BOLD which was initially dssigned for animals are not totally compatible in plants DNA barcoding research. Thus, we synthesize and customize a synopsis of technical notes and standards with reference of the BOLD criteria and experience of plant DNA barcoding projects, especial for the researchers with particular interest in plants DNA barcoding in China. Ten aspects related to plants DNA barcoding are covered: 1) sampling strategy for a plant DNA barcoding study, 2) collecting standards for vouches and associate information, 3) collection standards for specimenreferenced images, 4) collecting standards for DNA material, 5) standards for drying and preserving DNA material, 6) quality control and preservation procedures for extracted total genomic DNA, 7) recommended plant barcodes and universal primers, 8) procedures for PCR amplification and sequencing of the DNA barcodes, 9) naming,editing and submission for DNA barcoding files, and 10) procedures and methods for the analysis of DNA barcoding data.

    On the Methods and Principles of Molecular Identification of Chinese Herbs
    YUAN Qing-Jun-, ZHANG Wen-Jing-, JIANG Dan-, ZHANG Yong-Qing-, MA Chao-Yi-, HUANG Lu-Qi
    2012, 34(6):  607-613.  doi:10.3724/SP.J.1143.2012.12162
    Abstract ( 2166 )   HTML ( )   PDF (742KB) ( 2709 )   Save
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    Accurate identification of herbal medicinal materials is relevant to the safety of human life and economic interests. Traditional identification methods, including sensory evaluation, microscopic identification, physical and chemical identification, all have their limitations. Molecular identification brings a new opportunity for accurate identification of herbal medicinal materials. However, prior to its wide adoption, the methods and principles of molecular identification should be fully discussed. In this paper, we proposed a set of new methods for molecular authentication of herbal medicinal materials: 1) Identification between authenticity and adulteration by using specific polymerase chain reaction; 2) Identification between official herb and substitute by using the method of DNA barcoding; 3) Identification among multiple species of one official herbs by constructing genealogy among closelyrelated species based on population genetics; 4) Identification among herbs of different geographical origins by phylogeographybased analysis. For those that can not be identified by above four methods, more rapidly evolved markers such as microsatellite should be employed and individualbased analysis could be adopted.

    DNA Barcoding of Economically Important Mushrooms: A Case Study on Lethal Amanitas from China
    CA Qing, TANG Li-Ping, YANG Zhu-Liang
    2012, 34(6):  614-622.  doi:10.3724/SP.J.1143.2012.12140
    Abstract ( 2974 )   HTML ( )   PDF (4119KB) ( 2528 )   Save
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    Some species of the genus Amanita are economically important gourmet mushrooms, while others cause dramatic poisonings or even deaths every year in China and in many other countries. A DNA barcode is a short segment or a combination of short segments of DNA sequences that can distinguish species rapidly and accurately. To establish a standard DNA barcode for poisonous species of Amanita in China, three candidate markers, the large subunit nuclear ribosomal RNA (nLSU), the internal transcribed spacer (ITS), and the translation elongation factor 1alpha (tef1α) were tested using the eukaryotic general primers for their feasibility as barcodes to identify seven species of lethal fungi and two species of edible ones which can easily be confused with the lethal ones known from China. In addition, A.phalloides—a European and North American species closely related to one of the seven taxa, A.subjunquillea was also included. PCR amplification and sequencing success rate, intra and interspecific variation and rate of species identification were considered as main criteria for evaluation of the candidate DNA barcodes. Although the nLSU had high PCR and sequencing success rates (100% and 100% respectively), occasional overlapping occurred between the intra and interspecific variations. The PCR amplification and sequencing success rates of ITS were 100% and 85.7% respectively. ITS showed high sequence variation among species group and low variation within a given species. There was a relatively high PCR amplification and sequencing success rate for tef1α (85.7% and 100% respectively), and its intra and interspecific variation was higher than that of ITS or nLSU. All three candidate markers showed hight species resolution. ITS and tef1α had a more clearly defined barcode gap than nLSU. Our study showed that the tef1α and nLSU can be proposed as supplementary barcodes for the genus Amanita, while ITS can be used as a primary barcode marker considering that the ITS region may become a universal barcode marker for the fungal kingdom.

    A Framework of Scientific-Cloud for iFlora
    PENG Hui-Fu, WANG Yu-Hua
    2012, 34(6):  623-630.  doi:10.3724/SP.J.1143.2012.12139
    Abstract ( 3565 )   HTML ( )   PDF (1472KB) ( 2290 )   Save
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     In order to meet the broad requirements of the public and state departments to recognize and distinguish plant species, a plan for the nextgeneration Flora was proposed, which is internet, DNAsequence and informationtechnology based, i.e., iFlora. In this paper, we suggest and present a research framework of “ScientificCloud for iFlora”, which is a combination of ResourceCloud (Resource and Service layer), Intelligent Reorganization System, MobileClients (Application layer) and KeyUsers. (1) ResourceCloud: a collaborative working platform in the cloud site. This platform is used to integrate all relevant information resources, including DNA barcoding reference library, plant biodiversity information, and analysis models. (2) Intelligent Reorganization System of Virtualization: a system to retrieve, reorganize and present iFlorarecords of a given plant species automatically and intelligently. (3) MobileClients: software applications of mainstream mobile platforms, such as iOS, android and Windows phone. Constructed by these three parts, the framework will not only service for the key users with cooperating platform but also providing web service for the general public.
    The construction of this project will gradually combine botany and informatics. We are aiming to construct a sharing, easily accessible, and seamless connected ScientificCloud, with which numerous scientists cooperate together for iFlora. In addition, the ScientificCloud will integrate cognitive abilities of the machine, network, and taxonomists. It will provide an intelligent public service to perceive the plant world in a new dimension.