Presentation on theme: "Application of Bioinformatics in Plant Biodiversity P.N. Krishnan, Scientist & Coordinator Plant Biotechnology Division Bioinformatics Centre Tropical."— Presentation transcript:
Application of Bioinformatics in Plant Biodiversity P.N. Krishnan, Scientist & Coordinator Plant Biotechnology Division Bioinformatics Centre Tropical Botanic Garden and Research Institute Palode, Thiruvananthapuram Kerala, India Web site:http:/www.btisnet.nic.in/tbgri,
A LOOK AT WORLDS BIOLOGICAL RESOURCES 8 COUNTRIES RETAIN THEIR ORIGINAL FOREST; BRAZIL, CANADA AND RUSSIA ACCOUNT FOR 2/3 OF GLOBAL ORIGINAL FOREST TRACTS 76 COUNTRIES HAVE LOST THEIR ORIGINAL FORESTS COMPLETELY 28 COUNTRIES INCLUDING INDIA ARE LOOSING ORIGINAL VIRGIN FORESTS AND FACE SEVERE THREAT OF ECOLOGICAL IMBALANCE IF CONSERVATION EFFORTS ARE NOT TAKEN URGENTLY
Challenges facing the Humanity How to conserve the worlds' remaining natural resources
An advanced, integrated, planned, organized Data management Information processing Dissemination system For Implementing environmentally sound and sustainable utilization of the worlds natural resources
Such an information system can help in making Policies Plan Decision Implementations
Application of computers and information technology for collection, collation, storage, analysis, modeling, simulation and dissemination of diverse and distributed data / information about biotic resources and their environment
million life forms on earth 1.8 million species has been described by taxonomists With the current speed or scenario it will take 300 years to document all of them
INDIAS RESOURCES CategoryPercentage share Population16.0 Oil0.6 Gas0.5 Coal6.0 Cattle20.0 Buffaloes55.0 Biodiversity8.0 Land area2.2
What is Biodiversity Biodiversity refers to the variety and variability of living materials and ecological complexes in a given area and comprises species, genetic, and ecosystem diversity.
LEVELS OF BIODIVERSITY Molecular sequences Gene diversity Individuals Populations Species Higher taxa Habitats Ecosystems Biomes
Diversity is available in developing countries. But the information lies with developed countries
Megabiodiversity regions Mexico, Columbia, Equador, Peru, Brazil, Zaire, Medagascar, China, India, Malaysia, Indonesia, Australia
INDIA A MEGA DIVERSITY CENTRE AND A CENTRE OF CROP ORIGIN 2.4% LAND AREA HOLDS 8% OF WORLDS BIODIVERSITY; 10 TH AMONG PLANT RICH COUNTRIES OF THE WORLD; 4 TH AMONG COUNTRIES OF ASIA APPROXIMATELY 9000 HIGHER PLANT SPECIES OUT OF 17,000 ARE MEDICINAL PLANTS; 25-30% ARE ENDEMIC ABOUT 70% OF INDIAS POPULATION DEPEND ON PLANTS FOR PRIMARY HEALTHY CARE GREAT RAW MATERIAL (LOW VALUE) EXPORTER; 75% OF WORLDS PLANT BASED DRUGS COME FROM INDIAN PLANTS DIVERSITY WITHIN SPECIES (GENETIC DIVERSITY) IS RICH DUE TO DIVERSE SOIL AND ECO-CLIMATIC FACTORES; OVER POPULATED ; HABITAT DEGRADATION AND LOSSES COMMON; 27,500 HECTARES OF FOREST LAND DEPLETED ANNUALLY
India is one of the twelve megadiversity countries in the world In India species richness is often accompanied by enormous genetic diversity found within individual species. This makes India one of the Vavilovian Centres of diversity and origin of about 167 crop plants and the primary or secondary centres of domestication of a few animals.
Ecosystem wise, India has 42 vegetation types, 16 major forest types, 10 biogeographical zones and 25 hot spots of endemic centres
In India - about 5725 endemic taxa of angiosperm (33.5% of Indian flora) 1. Andaman group of islands 2. Nicobar group of islands 3. Agasthyamala hills 4. Anamala - high ranges 5. Palni hills 6. Nilgiris-Silent Valley-Wyanad-Kodagu 7. Shimoga-Kanara 8. Mahabaleshwar-Khandala Ranges 9. Konkan -Raigad 10. Marathwada-Satpura 11. Torupati-Cuddappa-Nallamalai hills 12. Vizagapatanam-Ganjam-Jeypore hills 13. Southern Deccan (leeward side) 14. Chotanagpur Plateau 15. Kathiawar-Kutch 16. Rajasthan-Aravalli hills 17. Khasia-Jaintia hills 18. Patkoi-Manipur-Lushai hills 19. Assam 20. Arunachal Pradesh Himalaya 21. Sikkim Himalayas 22. Garhwal-Kumaon Himalaya 23. Lahul-Himachal Pradesh Himalaya 24. Kashmir-Ladak Himalaya 25. Nepal Himalaya Hot spots of endemic species in India
INDIAS BIODIVESITY 1,26,188 species – cover all five Kingdoms 2.4% land area & 8% of global biodiversity Flowering plants:17,000 species Endemic species : 5,725 (33.5%)
Biological Spectrum of India
Western Ghats – Peaks Kalsubai m Banasuram m Vavulmala m Doddabetta m Devarmala m Anamudi m Agasthyamala m
Western Ghats – Vegetation types Southern tropical thorn forest – 300 m Southern tropical dry deciduous forest- 200 – 500 m Grasslands of lower altitudes – 500 m Southern tropical moist deciduous forest- 300 – 700 m Tropical semi-evergreen forest – 800 m Southern tropical wet-evergreen forest – 1500 m Subtropical montane forest- above 1500 m Grasslands of high altitudes- above 1500 m
Agasthyamala Flora Flora of the hot spot of Agasthyamala documented and published Total species documented species Endemic species- 317 species Wild relatives of crops- 100 species Important medicinal plants- 150 species
Red listed plants located - 27 New species described- 7 Rare species rediscovered- 8 Agasthyamala Flora Highlights
Lesser known fruit crops of the Western Ghats 150 sp. Recorded and documented Baccurea courtallense, Elaeocarpus serrtus and Flacoustia montana
Wild crop relatives of the Western Ghats Target species conserved at TBGRI Cinnamomum sp. Garcinia sp. Myristica sp. Syzygium sp. Curcuma sp. Zingiber sp.
Species - area relationship Silent Valley90 sq. km 1000 species Great Nicobar520 sq. km 771 species
Hottest of hot spots in India Eastern Himalayas Western Ghats
BIODIVERSITY AND ITS BENEFITS Agriculture Functioning ecosystem Economic value- extractable products, fuels, medicines, materials for shelter, food and energy Compounds, genes & species for industry Ecosystems- climate regulation, hydrological and chemical cycles in soils Recreation- social, ethical, spiritual, cultural and economic goods and services
Loss of Biodiversity due to Increasing population Spread of certain alien weeds affect native flora. Practice of shifting agriculture by local people. Selective harvesting of specific groups of plants for economic benefit. Developmental activities Tourists influx
CHALLENGES OF 21 ST CENTURY Bioresources are common resources Open access and lack of property rights No control on depletion Forests mostly under state control MNCs to privatize genes, gene products and transgenics
Biodiversity Convention, Trade related intellectual property rights (TRIPS) and General agreement on tariffs and trade(GATT)-give guidelines and regulations for biological resource use.
Convention on Biodiversity (CBD) –Article 15 Sovereign rights over genetic resources Facilitating access between contracting parties Access subject to mutually agreed terms and Access to prior informed consent Possible only if we have a high quality documentation We should initiate legal, administrative and scientific measures.
Biodiversity Conservation IN SITU and EX SITU
Biodiversity information is very complex, voluminous and rapidly proliferating. The biodiversity data can be categorised in to different types such as molecular sequences, gene diversity, individuals, species, higher taxa, population, habitats, ecosystems, biomes, etc. Management of complex and voluminous data of biodiversity is very difficult. Biodiversity data are scattered and not organised for further studies. At present it is very difficult to get a comprehensive picture of the genetic wealth of our nation. Application of Bioinformatics tools is the best solution to the above problems.
In Biodiversity we need Documentation Digitalization Networking Integration Coordination For achieving Individuals Organizations ( R&D, Govt.& NGOs)
What is Bioinformatics ? Bioinformatics is an emerging field of science growing from the application of mathematics, statistics, and information technology, including computers and the theory surrounding them, to the study and analysis of very large biological data. The field has been emerged for the management of massive data sets generated, and yet to be generated, in particular the data from the human genome project, as well as other genome projects. Bioinformatics uses computational algorithms for database creation, data management, data warehousing, data mining and global communication network.
How Bioinformatics intersects with and different aspects of the biological system Experiment Information Technology Computation Hardware & instrumentationMathematical & Physical Models DNA Sequence Gene & genome organisation Molecular evolution Protein structure, folding, function & interaction Metabolic pathways regulation Signaling Networks Physiology & cell biology Interspecies interaction Ecology & environment Biodiversity Methodology & Expertise Genome sequencing Genomic data analysis Statistical genetics Protein structure prediction, protein dynamics, protein folding and design Proteomics Functional genomics (microarrays, 2D-PAGE, etc.) High-tech field ecology Data standards, data representations, and analytical tools for complex biological data Dynamical system modelling Computational ecology Biodiversity data
OUR FIRST GOAL is: Know what you hold ? What are to be conserved? Where is it ? Why they be conserved? How much is it ? Where they be conserved? How much it worth ? How they be conserved?
The important applications of bioinformatics in biodiversity are: The complex and voluminous data of biodiversity can be digitalised for easy accession, analysis and interpretation. It makes easy survey, documentation and measurement of biodiversity data. Based on the available data, future biodiversity of a particular area can be predicted and model can be formulated by computational methods, thereby appropriate measures can be taken for its conservation and sustainable utilisation. It helps to predict species invasions using ecological niche modeling. The electronic information may serve as the raw material for augmenting future developments in all areas of biology. The digital databases can easily provide the current status of the biodiversity of a particular area.
The biodiversity extinction rate can be easily documented and theoretical studies and modeling can be formulated for its conservation on priority basis. The computational analysis makes easy understanding of the phylogenetic relationship among the species/individuals. Through internet biodiversity databases can be linked together and the information can be shared. The researchers can easily identify the priority materials for their studies. The potential indigenous material can be easily identified for biotechnological intervention.
*an estimated million known species. *one or two or more synonyms for every valid/accepted species *Compiling a list of scientific names for a major group takes years of effort. *Data gathered along with the name typically include the bibliographic reference, author(s), and date of publication, references to type specimens (institution and catalog number), type locality, and references to subsequent taxonomically significant publications.
Current status of Biodiversity information Biodiversity databases are highly diverse and heterogeneous, from genomic databases to specimen data bases to ecological and ecosystem data bases
Recently several web sites providing biodiversity information Biodiversity databases in the web can be broadly classified into the following groups Global databases Geographical, regional and national databases Databases for specific taxonomic group Government, scientific and advocacy organisations promoting biodiversity study Other resources.
Geographical, Regional and National Databases
Database for Specific Taxonomic Group
Tools and Software for Integrating Online Biodiversity Data
Government, Scientific, and Advocacy Organizations Promoting Biodiversity Study
INDIAN SCENARIO ATREE Sasya sahyadri-CD ROM NBRI Legume data base for South Asia NIO Marine prawns, crabs, mangroves,lignicolus fungi JN Centre for Advanced Studies Flora of Karnataka SACON Birds of India CSIR TKDL FRLHT Medicinal Plants TBGRI Plant Biodiversity Data bases, Wild Flowers of W.ghats, Indian Meliolales, Sacred groves of Kerala, Endemic plants of Kerala
To explore ways to combine data sets from different studies from habit to molecular levels if any in respect to any plant so that users can at least navigate across different studies made and the outcome of the same for the benefit of others.
During the 10 th plan period DBT has considered biodiversity informatics as one of the high priority areas.
Institutions specialised on biodiversity informatics under BTIS program
The aim of Bioinformatics Centre, TBGRI To organise a centralised digital database including all information related to biodiversity of India and sharing of these information for Research and Developments leading to conservation and sustainable utilisation of the plant genetic wealth and economic growth of the Nation as well as well being of the people.
Seed Pack version I A software for the management of Seed Bank data. Software Developed Bioinformatics Centre, TBGRI
The Seed List Page
Garden Info version I A software for the documentation and analysis of germplasm collection and maintenance data of botanic gardens. Software Developed Bioinformatics Centre, TBGRI
The Login Page Registered user - enter username and the password & access data New user - register by clicking the New user button.
The Plant List Page The List of all Plants in the Garden will be displayed Click on the plant name and see its details
Search Facility Search by Type, Family, Locality, Habit etc..
Data Entry Page
Passport Data Entry Page
Data Entry Page
Plant Info version I An Internet based database software for the management of all types of data related to biodiversity. The software is developed for organising a centralised digital database of the plant resources of our country. Software Developed Bioinformatics Centre, TBGRI
Plant Info version I Plant info database is developed in Structured Query Language (SQL) and to get dynamic content, the web site is created using Active Server Pages (ASP) and linked with Web Server.
PlantInfo Plant-Info Database Diagram
Only registered user can enter into the database Provided Login id and password to the registered users New user can register their membership Data will be provided on request Plant Info Home page
Plant Info administrative page User can search from left menu items and the search facility provided at the header. To add data of new plant click the link Add New Plant
Plant Info Data Documentation Page (Administrative page) Data fields arranged in four tabs - About Plant, Propagation, Drugs & Pests and Uses & Reports Combo-box selection facility is provided to avoid redundancy in data documentation *Marked fields are mandatory Image uploading facility
To add sub fields and document large volume of data, popup – windows with more fields are created Character formatting tools Popup window Character formatting tools
When click the Add link, Popup- window with sub fields will display Data fields in the tab Propagation Click
Data fields in the tab Propagation Popup window showing the sub fields when click the Add link cultivation
Data fields in the tab Drugs & Pests Click here Popup window with sub fields will display as shown below
Data fields in the tab Uses & Reports Click here Popup window with sub fields will display as shown below
Plant Info version I – Data view Page Data view – first page Provide dropdown menu and search facility to the quick accession of the data
Plant Info version I – Data view Page
Finger tip reference Plant Info version I – Data view Page
Search criteria Search by plant name Enter the plant name and click Go Search by Type Select a type from the combo-box Choose a sub type & click Go
Search by family Choose the family name from the combo-box and click Enter synonym & click Search by habit Select the habit and click
Left popyup menu for data accession Drop-down menu for data accession
Plant Info version I Special features User-friendly tools for the management and analysis of all types of data related to plant biodiversity. Advanced search facility Most powerful and flexible query wizard Navigation tools to access the information easily Illustrations and photographs Mouse over fingertip definition of each technical term Mouse over fingertip access to each reference Well protected security system Online interaction facility Platform for sharing data and data analysis Tutorial help support
In conclusion In Biological perspective, research findings on bioresources available and detailed studies on the plant biodiversity from A to Z available with the R&D Institutions and Universities should be pooled, synergized and made available in a format useful to various groups. In this case Initiative taken by TBGRI to make a centralized data base of the plant biodiversity of the GODS ON BIODIVERSITY RICH LAND may get momentum during the coming years.