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Biodiversity Information in the Web with special reference to spices Dr. Santhosh J. Eapen Bioinformatics Centre Indian Institute of Spices Research, Calicut-12.

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Presentation on theme: "Biodiversity Information in the Web with special reference to spices Dr. Santhosh J. Eapen Bioinformatics Centre Indian Institute of Spices Research, Calicut-12."— Presentation transcript:

1 Biodiversity Information in the Web with special reference to spices Dr. Santhosh J. Eapen Bioinformatics Centre Indian Institute of Spices Research, Calicut-12

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3 Beyond the specimen: genetic samples, field notes, images, recordings….

4 Biodiversity Data  The passport data management system handles basic information for each accession  The stock control system monitors incoming germplasm and the distribution of germplasm storage details of each accession  The evaluation data management system handles characterization data

5 Why Bioinformatics? To manage unprecedented, massive data To make information globally available and readily accessible to anybody - decision makers (Who uses the information….) To convert paper-based data to computer based (How information is used….)

6 How it helps……. Improve understanding of evolutionary processes underlying current diversity Improve use of biodiversity information in conservation BUT Depends crucially on connectivity of information Integration of systematics, biogeography, spatial modeling and genomics will:

7 Bioinformatics: Aims Organization of biological data (databases)databases Development of new tools to find solutions to biological problems (software)software Analyzing systematically different resources of biological data

8 Major Databases  GRIN – USDA ARS (www.ars.usda.gov/npgs) Gateway to GRIN (Germplasm Resource Information System)- Provides information about plants, animals, microbes and invertebrateswww.ars.usda.gov/npgs  SINGER (System-wide Information Network for Genetic Resources) – CGIAR (www.singer.cgiar.org) Genetic resources collected and conserved by the CGIAR centerswww.singer.cgiar.org  Biotica – (http://www.conabio.gob.mx) A Mexican biodiversity site for simple and reliable data capture of curatorial, nomenclatural, geographical and bibliographical datahttp://www.conabio.gob.mx  BCIS – Biodiversity Conservation Information System (http://www.biodiversity.org)http://www.biodiversity.org  GBIF – Global Biodiversity Information Facility (http://www.gbif.org) (http://www.gbif.org)  NatureServe – a network site on conservation (http://www.natureserve.org) (http://www.natureserve.org)  TOL - The Tree of Life (http://tolweb.org)http://tolweb.org

9 Crop Based Databases Barley Germplasm Database (www.grs.nig.ac.jp/barley)(www.grs.nig.ac.jp/barley) Graingenes (Database on Triticeae and Avena)– USDA-ARS (http://wheat.pw.usda.gov) (http://wheat.pw.usda.gov) Komugi (Integrated Wheat Science Database) – National Institute of Genetics, Japan (http://shigen.lab.nig.ac,jp/wheat/komugi) (http://shigen.lab.nig.ac,jp/wheat/komugi) Oryzabase (Integrated Rice Science Database) – National Institute of Genetics, Japan (http://shigen.lab.nig.ac.jp/rice/oryzabase)http://shigen.lab.nig.ac.jp/rice/oryzabase MGIS (Musa Germplasm Information System) – INIBAP (http://www.inibap.org/research/mgis_eng.htm)http://www.inibap.org/research/mgis_eng.htm ICGD – International Cocoa Germplasm Database (http://www.icdg.rdg.ac.uk) (http://www.icdg.rdg.ac.uk)

10 Electronic Catalogues Species 2000 (http://www.sp2000.org)http://www.sp2000.org ITIS – Integrated Taxonomic Information System (http://www.itis.usda.gov) (http://www.itis.usda.gov) IPNI - The International Plant Names Index (http://www.ipni.org)http://www.ipni.org

11 Biodiversity Software BioLink – from CSIRO, Australia (http://www.ento.CSIRO.au/biolink/software.html)http://www.ento.CSIRO.au/biolink/software.html Biota – a biodiversity database manager from University of Connecticut (http://www.viceroy.eeb.uconn.edu/biotapages/download.html)http://www.viceroy.eeb.uconn.edu/biotapages/download.html DELTA – DEscription Language for TAxonomy (http://www.biodiversity.bio.uno.edu/delta) (http://www.biodiversity.bio.uno.edu/delta) PAUP – A phylogeny analysis software (http://www.paup.csit.fsu.edu/downl.html) (http://www.paup.csit.fsu.edu/downl.html) SPECIFY (http://usobi.org/specify)http://usobi.org/specify

12 Other Efforts National Microbial Germplasm Project – USDA (www.ars.usda.gov/nmg)www.ars.usda.gov/nmg MGD - Microbial Germplasm Database (www.mgd.nacse.org)www.mgd.nacse.org

13 IISR Initiatives…… SPICEGENES –Black PepperBlack Pepper –TurmericTurmeric –NutmegNutmeg PIR (Phytophthora Information Resource)Phytophthora PiperBase

14 World Distribution of Piper  Central and South America (New world)  India, Malaysia, Indonesia and Sri Lanka (Old World) India: Two independent Centers 1.Western Ghats 2. North East Region Black Pepper Genetic Resources- A case study

15 Indian Gene Centre: Present status One of the 12 megadiversity centres Two hot spots Northeastern Himalayas Western Ghats

16 Biodiversity of Piper specis South American Species: Shrubs or trees (monoecious) Indian Species: Woody vines or creepers (dioceious) Monoecious (rare)- P.silentvalleyensis from Nilgiris and Silent valley). Intermediate types from Idukki districts Cultivated Piper – Originated from the wild ones as a result of continuous selection and vegetative propogation by man over ages

17 Species Diversity of Piper in Western Ghats P.argyrophyllum MiqP.barberi Gamble P.attenuatum Buch-Ham P.betle Linn P.galeatum (miq) CDCP.hapnium Ham P.hymenophyllum MiqP.hookeri Miq P.longum LinnP.mullesua Ham P.nigrum LinnP.pseudonigrum Velayudhan P.schmidtii Hook f.P.silentvalleyensis Ravindran P.sugandhi Ravindran & Babu P.trichostachyon CDCP.wightii Miq

18 P.longum-male

19 P.hapnium

20 P.mullesua

21 P.schmidtii

22 P.wightii

23 Species diversity in NE Region P.griffithi Cas DCP.muricatum var.glaberata Griffith P.peepuloides RoxbP.betle Linn P.boehmeriaefolium Wall.CatP.hamiltonii Cas DC P.aurantiacum WallP.khasianum Cas P.petiolatum Hook.f.P.chaba H. P.sylvaticum RoxbP.thomsoni Hook

24 P.chaba

25 P.silvaticum

26 P.colubrinum P.ornatum EXOTIC COLLECTIONS

27 Cultivar diversity in black pepper AimpiriyanArakkulammundaBalankotta BilimallegesaraChengannurkodiCheppakulamindi CheriyakaniyakadanJeerakamundiKalluvally KarimundaKottanKottanadan KutchingKurimalaiKuthiravali KuttianikodiMalamundiMallegesara NarayakodiNeelamundiNedumchola NeyyattinkaramundiPerambramundaPerumkodi PoonjaranmundaThommankodiThevanmundi ThulamundiUddagaraVadakkan ValiyakaniyakkadanVattamundiVellanamban

28 Black pepper germplasm conserved at IISR Wild Accession962 BP Cultivars969 Karimunda accessions200 Kottanadan accessions68 Total2199 Sl.NoCentreCultivatedWildTotal 1PRS, Panniyur PRS, Sirsi RARS, Chintappally HRS, Yercaud Black pepper germplasm at AICRP-Spices Centers

29 View table Passport Details- Cultivars

30 DATA SHEET FOR WILD Piper

31 Evaluation Data sheet- Cultivara

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