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Application of Bioinformatics in Plant Biodiversity

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1 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,

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 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

3 Challenges facing the Humanity
How to conserve the worlds' remaining natural resources

4 An advanced, integrated, planned, organized
Data management Information processing Dissemination system For Implementing environmentally sound and sustainable utilization of the world’s natural resources

5 Such an information system can help in making
Policies Plan Decision Implementations

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 taxonomists With 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
Gas Coal Cattle Buffaloes Biodiversity 8.0 Land area 2.2

9 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.

10 LEVELS OF BIODIVERSITY
Molecular sequences Gene diversity Individuals Populations Species Higher taxa Habitats Ecosystems Biomes

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; 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

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 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

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%)

18 Biological Spectrum of India

19 Western Ghats – Peaks Kalsubai - 1646 m Banasuram - 2060 m
Vavulmala m Doddabetta m Devarmala m Anamudi m Agasthyamala m

20 Western Ghats – Vegetation types
Southern tropical thorn forest – 300 m Southern tropical dry deciduous forest – 500 m Grasslands of lower altitudes – 500 m Southern tropical moist deciduous forest – 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

21 Western Ghats – Floristic diversity
Angiosperms – 4000 sp. Gymnosperms – sp. Pteridophytes – sp. Bryophytes – sp. Lichens – sp. Algae – sp. Fungi – 5500 sp.

22 Angiosperms – groups Trees – 1250 sp. Epiphytes – 150 sp.
Parasites – sp. Insectivorous – sp. Saprophytes – sp. Aquatic – sp.

23 Western Ghats- Endemism
Total species sp. Endemic sp. Agasthyamala sp. Nilgiri-Silent Valley sp. Nayar

24 Western Ghats - Wild crop relatives
Zingiber sp. Curcuma sp. Garcinia sp. Cinnamomum sp. Syzygium sp. Dioscorea sp. Amorphophallus sp.

25 Flora of the hot spot of Agasthyamala documented and published
Agasthyamala Flora Flora of the hot spot of Agasthyamala documented and published Total species documented species Endemic species species Wild relatives of crops species Important medicinal plants species

26 Agasthyamala Flora Highlights Red listed plants located - 27
Red listed plants located - 27 New species described - 7 Rare species rediscovered - 8

27 Lesser known fruit crops of the Western Ghats
150 sp. Recorded and documented Baccurea courtallense, Elaeocarpus serrtus and Flacoustia montana

28 Wild crop relatives of the
Western Ghats Target species conserved at TBGRI Cinnamomum sp. Garcinia sp. Myristica sp. Syzygium sp. Curcuma sp. Zingiber sp.

29 Species - area relationship
Silent Valley 90 sq. km 1000 species Great Nicobar 520 sq. km 771 species

30 Hottest of hot spots in India
Eastern Himalayas Western Ghats

31 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

32 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

33 CHALLENGES OF 21ST 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

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 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.

36 Biodiversity Conservation
IN SITU and EX SITU

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
Documentation Digitalization Networking Integration Coordination For achieving Individuals Organizations ( 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 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

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 groups Global databases Geographical, regional and national databases Databases for specific taxonomic group Government, scientific and advocacy organisations promoting biodiversity study Other resources.

47 Global databases

48 Geographical, Regional and National Databases

49 Database for Specific Taxonomic Group

50 Database for Specific Taxonomic Group

51 Database for Specific Taxonomic Group

52 Tools and Software for Integrating Online Biodiversity Data

53 Government, Scientific, and Advocacy Organizations Promoting Biodiversity Study

54 Government, Scientific, and Advocacy Organizations Promoting Biodiversity Study

55 Other Resources

56 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

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 Developed Seed Pack version I A software for the management of Seed Bank data.

62 Login Page

63 The Seed List Page

64 Search Facility

65 Bioinformatics Centre , TBGRI
Software Developed Garden Info version I A software for the documentation and analysis of germplasm collection and maintenance data of botanic gardens.

66 Administration Page

67 The Login Page Registered user - enter username and the password & access data New user - register by clicking the “New user” button.

68 The Plant List Page The List of all Plants in the Garden will be displayed Click on the plant name and see its details

69 Search by Type , Family , Locality, Habit etc..
Search Facility Search by Type , Family , Locality, Habit etc..

70 Data Entry Page

71 Passport Data Entry Page

72 Data Entry Page

73

74 Bioinformatics Centre , TBGRI
Software Developed 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.

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.

76 PlantInfo Plant-Info Database Diagram

77 Plant Info Home page 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

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 mandatory Image uploading facility

80 Combo-box selection

81 Character formatting tools
Popup window Character formatting tools To add sub fields and document large volume of data, popup – windows with more fields are created Character formatting tools

82 Data fields in the tab Propagation
Click When click the ‘Add’ link, Popup- window with sub fields will display

83 Data fields in the tab Propagation
Popup window showing the sub fields when click the ‘Add’ link cultivation

84 Data fields in the tab Drugs & Pests
Click here Popup window with sub fields will display as shown below

85 Data fields in the tab Uses & Reports
Click here Popup window with sub fields will display as shown below

86 Plant Info version I – Data view Page
Data view – first page Provide dropdown menu and search facility to the quick accession of the data

87 Plant Info version I – Data view Page

88 Plant Info version I – Data view Page

89 Plant Info version I – Data view Page

90 Plant Info version I – Data view Page

91 Plant Info version I – Data view Page

92 Plant Info version I – Data view Page

93 Plant Info version I – Data view Page

94 Plant Info version I – Data view Page

95 Plant Info version I – Data view Page

96 Plant Info version I – Data view Page

97 Plant Info version I – Data view Page
Finger tip reference

98 Plant Info version I – Data view Page

99 Plant Info version I – Data view Page

100 Plant Info version I – Data view Page

101 Plant Info version I – Data view Page

102 Search criteria Search by Type Select a type from the combo-box
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

103 Search by family Choose the family name from the combo-box and click Enter synonym & click Search by habit Select the habit and click

104 Left popyup menu for data accession
Drop-down menu for data accession Left 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 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

106 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 GOD’S ON BIODIVERSITY RICH LAND may get momentum during the coming years.

107 For a green and clean nature
With Best Wishes for 2005 For a green and clean nature Thank you


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