Presentation on theme: "Application of Bioinformatics in Plant Biodiversity"— Presentation transcript:
1 Application of Bioinformatics in Plant Biodiversity P.N. Krishnan,Scientist & CoordinatorPlant Biotechnology DivisionBioinformatics CentreTropical Botanic Garden and Research InstitutePalode, ThiruvananthapuramKerala, IndiaWeb site:http:/www.btisnet.nic.in/tbgri,
2 A LOOK AT WORLDS’ BIOLOGICAL RESOURCES 8 COUNTRIES RETAIN THEIR ORIGINAL FOREST; BRAZIL, CANADA AND RUSSIA ACCOUNT FOR 2/3 OF GLOBAL ORIGINAL FOREST TRACTS76 COUNTRIES HAVE LOST THEIR ORIGINAL FORESTS COMPLETELY28 COUNTRIES INCLUDING INDIA ARE LOOSING ORIGINAL VIRGIN FORESTS AND FACE SEVERE THREAT OF ECOLOGICAL IMBALANCE IF CONSERVATION EFFORTS ARE NOT TAKEN URGENTLY
3 Challenges facing the Humanity How to conserve the worlds' remaining natural resources
4 An advanced, integrated, planned, organized Data managementInformation processingDissemination systemFor Implementing environmentally sound and sustainable utilization of the world’s natural resources
5 Such an information system can help in making PoliciesPlanDecisionImplementations
6 Application of computers and information 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
7 10-100 million life forms on earth 1.8 million species has been described by taxonomistsWith the current speed or scenario it will take 300 years to document all of them
8 INDIA’S RESOURCES Category Percentage share Population 16.0 Oil 0.6 GasCoalCattleBuffaloesBiodiversity 8.0Land area 2.2
9 What is BiodiversityBiodiversity refers to the variety and variability of living materials and ecological complexes in a given area and comprises species, genetic, and ecosystem diversity.
10 LEVELS OF BIODIVERSITY Molecular sequencesGene diversityIndividualsPopulationsSpeciesHigher taxaHabitatsEcosystemsBiomes
11 Diversity is available in developing countries. But the information lies with developed countries
12 Megabiodiversity regions Mexico, Columbia, Equador, Peru, Brazil, Zaire, Medagascar, China, India, Malaysia, Indonesia, Australia
13 INDIA A MEGA DIVERSITY CENTRE AND A CENTRE OF CROP ORIGIN 2.4% LAND AREA HOLDS 8% OF WORLDS BIODIVERSITY; 10THAMONG PLANT RICH COUNTRIES OF THE WORLD; 4TH AMONGCOUNTRIES OF ASIAAPPROXIMATELY 9000 HIGHER PLANT SPECIES OUT OF 17,000ARE MEDICINAL PLANTS; 25-30% ARE ENDEMICABOUT 70% OF INDIA’S POPULATION DEPEND ON PLANTS FORPRIMARY HEALTHY CAREGREAT RAW MATERIAL (LOW VALUE) EXPORTER; 75% OFWORLDS PLANT BASED DRUGS COME FROM INDIAN PLANTSDIVERSITY WITHIN SPECIES (GENETIC DIVERSITY) IS RICH DUETO DIVERSE SOIL AND ECO-CLIMATIC FACTORES; OVERPOPULATED ; HABITAT DEGRADATION AND LOSSES COMMON;27,500 HECTARES OF FOREST LAND DEPLETED ANNUALLY
14 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.
15 Ecosystem wise, India has 42 vegetation types, 16 major forest types, 10 biogeographical zones and 25 hot spots of endemic centres
16 Hot spots of endemic species in India In India - about 5725 endemic taxa of angiosperm (33.5% of Indian flora)Hot spots of endemic species in India1. Andaman group of islands2. Nicobar group of islands3. Agasthyamala hills4. Anamala - high ranges5. Palni hills6. Nilgiris-Silent Valley-Wyanad-Kodagu7. Shimoga-Kanara8. Mahabaleshwar-Khandala Ranges9. Konkan -Raigad10. Marathwada-Satpura11. Torupati-Cuddappa-Nallamalai hills12. Vizagapatanam-Ganjam-Jeypore hills13. Southern Deccan (leeward side)14. Chotanagpur Plateau15. Kathiawar-Kutch16. Rajasthan-Aravalli hills17. Khasia-Jaintia hills18. Patkoi-Manipur-Lushai hills19. Assam20. Arunachal Pradesh Himalaya21. Sikkim Himalayas22. Garhwal-Kumaon Himalaya23. Lahul-Himachal Pradesh Himalaya24. Kashmir-Ladak Himalaya25. Nepal Himalaya
17 INDIAS BIODIVESITY 1,26,188 species – cover all five Kingdoms. 2 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 : ,725 (33.5%)
25 Flora of the hot spot of Agasthyamala documented and published Agasthyamala FloraFlora of the hot spot of Agasthyamala documented and publishedTotal species documented speciesEndemic species speciesWild relatives of crops speciesImportant medicinal plants species
26 Agasthyamala Flora Highlights Red listed plants located - 27 Red listed plants located - 27New species described - 7Rare species rediscovered - 8
27 Lesser known fruit crops of the Western Ghats 150 sp. Recorded and documentedBaccurea courtallense, Elaeocarpus serrtus and Flacoustia montana
28 Wild crop relatives of the Western GhatsTarget species conserved at TBGRICinnamomum sp.Garcinia sp.Myristica sp.Syzygium sp.Curcuma sp.Zingiber sp.
29 Species - area relationship Silent Valley 90 sq. km 1000 speciesGreat Nicobar 520 sq. km 771 species
30 Hottest of hot spots in India Eastern HimalayasWestern Ghats
31 BIODIVERSITY AND ITS BENEFITS AgricultureFunctioning ecosystemEconomic value- extractable products, fuels, medicines, materials for shelter, food and energyCompounds, genes & species for industryEcosystems- climate regulation, hydrological and chemical cycles in soilsRecreation- social, ethical, spiritual, cultural and economic goods and services
32 Loss of Biodiversity due to Increasing populationSpread 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 activitiesTourists influx
33 CHALLENGES OF 21ST CENTURY Bioresources are common resources Open access and lack of property rightsNo control on depletionForests mostly under state controlMNCs to privatize genes , geneproducts and transgenics
34 Biodiversity Convention, Trade related intellectual property rights (TRIPS) and General agreement on tariffs and trade(GATT)-give guidelines and regulations for biological resource use.
35 Convention on Biodiversity (CBD) –Article 15 Sovereign rights over genetic resourcesFacilitating access between contracting partiesAccess subject to mutually agreed terms andAccess to prior informed consentPossible only if we have a high quality documentationWe should initiate legal, administrative and scientific measures.
37 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.
38 In Biodiversity we need DocumentationDigitalizationNetworkingIntegrationCoordinationFor achievingIndividualsOrganizations ( R&D, Govt.& NGOs)
39 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.
40 Mathematical & Physical Models How Bioinformatics intersects with and different aspects of the biological systemExperimentComputationInformation TechnologyHardware & instrumentationMathematical & Physical ModelsDNA SequenceGene & genome organisationMolecular evolutionProtein structure, folding, function & interactionMetabolic pathways regulationSignalingNetworksPhysiology & cell biologyInterspecies interactionEcology & environmentBiodiversityMethodology & ExpertiseGenome sequencingStatistical geneticsGenomic data analysisProteomicsProtein structure prediction, protein dynamics, protein folding and designFunctional genomics (microarrays, 2D-PAGE, etc.)Data standards, data representations, and analytical tools for complex biological dataDynamical system modellingHigh-tech field ecologyBiodiversity dataComputational ecology
41 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?
42 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.
43 The biodiversity extinction rate can be easily documented 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.
44 *an estimated 1.5 - 2 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.
45 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
46 Recently several web sites providing biodiversity information Biodiversity databases in the web can be broadly classified into the following groupsGlobal databasesGeographical, regional and national databasesDatabases for specific taxonomic groupGovernment, scientific and advocacy organisations promoting biodiversity studyOther resources.
56 INDIAN SCENARIO ATREE Sasya sahyadri-CD ROM NBRI Legume data base for South AsiaNIO Marine prawns, crabs, mangroves,lignicolus fungiJN Centre for Advanced Studies Flora of KarnatakaSACON Birds of IndiaCSIR TKDLFRLHT Medicinal PlantsTBGRI Plant Biodiversity Data bases, Wild Flowers of W.ghats, Indian Meliolales, Sacred groves of Kerala, Endemic plants of Kerala
57 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.
58 During the 10th plan period DBT has considered biodiversity informatics as one of the high priority areas.
59 Institutions specialised on biodiversity informatics under BTIS program
60 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.
61 Bioinformatics Centre , TBGRI Software DevelopedSeed Pack version IA software for the management of Seed Bank data.
74 Bioinformatics Centre , TBGRI Software DevelopedPlant Info version IAn 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.
75 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.
77 Plant Info Home pageOnly registered user can enter into the databaseProvided Login id and password to the registered usersNew user can register their membershipData will be provided on request
78 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’
79 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 mandatoryImage uploading facility
102 Search criteria Search by Type Select a type from the combo-box Search by plant nameEnter the plant name and click GoSearch by TypeSelect a type from the combo-boxChoose a sub type & click Go
103 Search by familyChoose the family name from the combo-box and clickEnter synonym & clickSearch by habitSelect the habit and click
104 Left popyup menu for data accession Drop-down menu for data accessionLeft popyup menu for data accession
105 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 facilityMost powerful and flexible query wizardNavigation tools to access the information easilyIllustrations and photographsMouse over fingertip definition of each technical termMouse over fingertip access to each referenceWell protected security systemOnline interaction facilityPlatform for sharing data and data analysisTutorial help support
106 In conclusionIn 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 GOD’S ON BIODIVERSITY RICH LAND may get momentum during the coming years.
107 For a green and clean nature With Best Wishes for 2005For a green and clean natureThank you