Application of Bioinformatics in Plant Biodiversity • P.N. Krishnan, • Scientist & Coordinator • Plant Biotechnology Division • Bioinformatics Centre • Tropical Botanic Garden and Research Institute • Palode, Thiruvananthapuram - 695 562 • Kerala, India • Web site:http:/www.btisnet.nic.in/tbgri, http:/www.tbgri.org • E-mail:firstname.lastname@example.org
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 world’s 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
10-100 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
INDIA’S RESOURCES Category Percentage share Population 16.0 Oil 0.6 Gas 0.5 Coal 6.0 Cattle 20.0 Buffaloes 55.0 Biodiversity 8.0 Land area 2.2
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; 10TH • AMONG PLANT RICH COUNTRIES OF THE WORLD; 4TH AMONG • COUNTRIES OF ASIA • APPROXIMATELY 9000 HIGHER PLANT SPECIES OUT OF 17,000 • ARE MEDICINAL PLANTS; 25-30% ARE ENDEMIC • ABOUT 70% OF INDIA’S 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) Hot spots of endemic species in India 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
INDIAS BIODIVESITY1,26,188 species – cover all five Kingdoms 2.4% land area & 8% of global biodiversityFlowering plants : 17,000 species Endemic species : 5,725 (33.5%)
Western Ghats – Peaks Kalsubai - 1646 m Banasuram - 2060 m Vavulmala - 2339 m Doddabetta - 2637 m Devarmala - 1922 m Anamudi - 2695 m Agasthyamala - 1868 m
Southern tropical thorn forest - 200 – 300 m Southern tropical dry deciduous forest - 200 – 500 m Grasslands of lower altitudes - 200 – 500 m Southern tropical moist deciduous forest - 300 – 700 m Tropical semi-evergreen forest - 500 – 800 m Southern tropical wet-evergreen forest - 800 – 1500 m Subtropical montane forest - above 1500 m Grasslands of high altitudes - above 1500 m Western Ghats – Vegetation types
Western Ghats – Floristic diversity • Angiosperms – 4000 sp. • Gymnosperms – 4 sp. • Pteridophytes – 350 sp. • Bryophytes – 400 sp. • Lichens – 550 sp. • Algae – 400 sp. • Fungi – 5500 sp.
Angiosperms – groups • Trees – 1250 sp. • Epiphytes – 150 sp. • Parasites – 75 sp. • Insectivorous – 30 sp. • Saprophytes – 5 sp. • Aquatic – 200 sp.
Western Ghats- Endemism Total species - 4000 sp. Endemic - 1500 sp. Agasthyamala - 189 sp. Nilgiri-Silent Valley - 150 sp. Nayar - 1997
Western Ghats - Wild crop relatives Zingiber - 8 sp. Curcuma - 20 sp. Garcinia - 10 sp. Cinnamomum - 15 sp. Syzygium - 20 sp. Dioscorea - 15 sp. Amorphophallus - 8 sp.
Agasthyamala Flora Flora of the hot spot of Agasthyamala documented and published Total species documented - 1200 species Endemic species - 317 species Wild relatives of crops - 100 species Important medicinal plants - 150 species
Agasthyamala Flora Highlights • Red listed plants located - 27 • New species described - 7 • Rare species rediscovered - 8
Lesser known fruit crops of theWestern 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 Valley 90 sq. km 1000 species Great Nicobar 520 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 21ST CENTURY Bioresources are common resources • Open access and lack of property rights • No control on depletion • Forests mostlyunder 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 Computation Information Technology Hardware & instrumentation Mathematical & 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 Statistical genetics Genomic data analysis Proteomics Protein structure prediction, protein dynamics, protein folding and design Functional genomics (microarrays, 2D-PAGE, etc.) Data standards, data representations, and analytical tools for complex biological data Dynamical system modelling High-tech field ecology Biodiversity data Computational ecology
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 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.
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.