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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 Slide 2 Slide 3 Beyond the specimen: genetic samples, field notes, images, recordings. Slide 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 Slide 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.) Slide 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: Slide 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 Slide 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 Slide 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) Slide 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 Slide 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 Slide 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 Slide 13 IISR Initiatives SPICEGENES Black PepperBlack Pepper TurmericTurmeric NutmegNutmeg PIR (Phytophthora Information Resource)Phytophthora PiperBase Slide 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 Slide 15 Indian Gene Centre: Present status One of the 12 megadiversity centres Two hot spots Northeastern Himalayas Western Ghats Slide 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 Slide 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 Slide 18 P.longum-male Slide 19 P.hapnium Slide 20 P.mullesua Slide 21 P.schmidtii Slide 22 P.wightii Slide 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 Slide 24 P.chaba Slide 25 P.silvaticum Slide 26 P.colubrinum P.ornatum EXOTIC COLLECTIONS Slide 27 Cultivar diversity in black pepper AimpiriyanArakkulammundaBalankotta BilimallegesaraChengannurkodiCheppakulamindi CheriyakaniyakadanJeerakamundiKalluvally KarimundaKottanKottanadan KutchingKurimalaiKuthiravali KuttianikodiMalamundiMallegesara NarayakodiNeelamundiNedumchola NeyyattinkaramundiPerambramundaPerumkodi PoonjaranmundaThommankodiThevanmundi ThulamundiUddagaraVadakkan ValiyakaniyakkadanVattamundiVellanamban Slide 28 Black pepper germplasm conserved at IISR Wild Accession962 BP Cultivars969 Karimunda accessions200 Kottanadan accessions68 Total2199 Sl.NoCentreCultivatedWildTotal 1PRS, Panniyur138--138 2PRS, Sirsi752196 3RARS, Chintappally262955 4HRS, Yercaud106--106 Black pepper germplasm at AICRP-Spices Centers Slide 29 View table Passport Details- Cultivars Slide 30 DATA SHEET FOR WILD Piper Slide 31 Evaluation Data sheet- Cultivara Slide 32 Slide 33 Slide 34