Taxonomic Identification And Application Mode In Molecular Biology Of Pleuronectiformes

Since the beginning of the 21st Century, international organizations specializing in fishery, ecology and environmental protection, and systemics studies have been attaching primary importance to taxonomy for its fundamental role in biodiversity studies. Protocols on unearthing and sharing taxonomic information have become a hotspot issue of the Global Taxonomy Initiative (GTI) under the Convention on Biological Diversity (CBD). GTI spares no effort to tackle the"taxonomic impediment"which seriously hinders the taxonomic applications to the sustained exploitation of natural biological resources. Henceforth the digital taxonomic information system has been promoted at such an accelerated speed that it is inevitable to digitalize storage of existing knowledge, share the network and standardize the integrated data. However, following Linnaeus, almost all research results on classification were kept in printed format with abundant contents, rich types, complex structures and plentiful numbers of languages. At present, taxonomic data still scatters in different subject databases with most technical literature slumbering in libraries, museums and archives. The fact that few types of software are designed for exploitation and digitalization of the traditional taxonomic information, especially the lack of a system to bridge the traditional taxonomic data and the molecular sequences, increases the difficulty in connecting various data for comprehensive applications.Pleuronectiformes(flatfish)is an order with special asymmetric shape and structure, and a long complicated history of evolution. Many species of the order are of great importance to the local economy for their valuable relish. Taxonomy research is meaningful for both biological studies and aquaculture production, but up to now the taxonomic system remains unintegrated.For exploring the methods to integrate all of the taxonomic information of the specific taxa under a Windows application, this thesis develops a program named"Pleuronectiformes Taxonomy Information Analysis System (PTIAS)"(National copyright registration number: 2009SR02219) to find out the techniques for bridging and transforming taxa/taxon taxonomic information to specialized corresponding formats,such as taxonomy system, identification keys, molecular markers, DNA barcodes, phylogeny tree, bibliographies and other taxonomic references.1. Illustrate the method of constructing taxonomic data modules for PTIAS. Based on taxonomy outputs of GTI scheme from 2008 to 2020, the thesis first built a comprehensive evaluation module by fuzzy analysis, then evaluated, selected and categorized data sources with a standpoint of taxonomy, and then analyzed the structure, content and relations among various databases, and finally designed a metadata and index system with a database module for PTIAS.2. Design a digital taxonomy system module for integrating different taxonomic catalogs from GTI databases to PTIAS. Based on treeview database, the thesis established an extendable stratum module, able to stretch to all taxon levels and compose any taxon or taxa combination to bridge taxonomic information. The module is designed as the basic component for data connection, comparably analysis, database reconstruction and other data processing of certain species group dynamically designated.3. Devise a BiosKey algorithm for traditional identification keys and Cladistics Trackback System of PTIAS. Based on keys in printed format and attributes of datawindow, the thesis studies a concise tree module, extendable to display pictures of shape characteristics of flatfishes, and able to apply in multi-key searching, forming an index mechanism for deriving terminology words from original keys. The necessity of distinguishing structure of dichotomous key from binary tree is discussed, since there is no sub node with priority of order or comparable values in the same level during the procession of dichotomous grouping. For probing the possibility of integrating necessary information of phylogenetic systems and Linnaean system and even identification keys, a digital Cladistics Traceback System is suggested to be used for integrating various system viewpoints based on the similar tree data structure, the collective taxa strata and the completely unified species taxon of all systems.4. Present a visual hot-key index module for molecular markers of PTIAS. Based on genome structure of mtDNA and nDNA, the graphic markers are put into datawindow as functional buttons of indexes for retrieving sequence records. Each hot-key is traced by the mousemove function, and is bound to retrieving indexes and data of DNA barcodes, molecular markers and the taxonomic catalog when activated.5. Study on a rapid processing method for large database and build an optimized the local environment for Blast, Clustal W and Phylip package with different MS-DOS modes under Windows system. For accelerating date retrieving, data extracting and database reconstructing, data-store technique was infixed to file mapping process to lead indexes searching into data blocks of memory. Using a settable small amount of buffer, the rapid method could completely overcome the choke point of I/O and memory when dealing with big files.6. Research on the method of designing a system and the construction of using platform modules for different taxonomic information. The 9 data modules, 9 taxonomic functional modules and 3 data processing service modules are separately designed and integrated in PTIAS. All of the standardized data functions orderly for platform initialization, databases, indexes, and the taxonomic formats automatically transformed by the built-in program functions such as Linnaean system, identification key, molecular sequence table and phylogenetic tree, as well as initialization parameters for visible or invisible controls like datawindows, dropdown lists and dynamic datastores, etc..7. Scheme an online data retrieving, editing and extracting method for GTI taxonomic databases. Microsoft web browse active control is employed to develop the component of taxonomic reference information module, and indexes for GTI portals are used to bridge taxonomy catalog and bind information.