Biodiversity Information in the Web with special reference to spices

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Biodiversity Information in the Webwith special
reference to spices

• Dr. Santhosh J. Eapen

Bioinformatics Centre Indian Institute of Spices
Research, Calicut-12
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Beyond the specimen genetic samples, field
notes, images, recordings.
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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

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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.)

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How it helps.
Integration of systematics, biogeography, spatial
modeling and genomics will

• Improve understanding of evolutionary processes
  underlying current diversity
• Improve use of biodiversity information in
  conservation BUT
• Depends crucially on connectivity of information

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Bioinformatics Aims

• Organization of biological data (databases)
• Development of new tools to find solutions to
  biological problems (software)
• Analyzing systematically different resources of
  biological data

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Major Databases

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

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Crop Based Databases

• Barley Germplasm Database (www.grs.nig.ac.jp/barle
  y)
• Graingenes (Database on Triticeae and Avena)
  USDA-ARS (http//wheat.pw.usda.gov)
• Komugi (Integrated Wheat Science Database)
  National Institute of Genetics, Japan
  (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)
• MGIS (Musa Germplasm Information System) INIBAP
  (http//www.inibap.org/research/mgis_eng.htm)
• ICGD International Cocoa Germplasm Database
  (http//www.icdg.rdg.ac.uk)

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Electronic Catalogues

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

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Biodiversity Software

• BioLink from CSIRO, Australia
  (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)
• DELTA DEscription Language for TAxonomy
  (http//www.biodiversity.bio.uno.edu/delta)
• PAUP A phylogeny analysis software
  (http//www.paup.csit.fsu.edu/downl.html)
• SPECIFY (http//usobi.org/specify)

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Other Efforts

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

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IISR Initiatives

• SPICEGENES
• Black Pepper
• Turmeric
• Nutmeg
• PIR (Phytophthora Information Resource)
• PiperBase

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Black Pepper Genetic Resources- A case study
World Distribution of Piper

• Central and South America (New world)
• India, Malaysia, Indonesia and Sri Lanka (Old
  World)
• India Two independent Centers
• Western Ghats
• 2. North East Region

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• Indian Gene Centre Present status
• One of the 12 megadiversity centres
• Two hot spots

• Western Ghats

• Northeastern Himalayas

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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

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Species Diversity of Piper in Western Ghats
P.argyrophyllum Miq P.barberi
Gamble P.attenuatum Buch-Ham P.betle
Linn P.galeatum (miq) CDC P.hapnium
Ham P.hymenophyllum Miq P.hookeri Miq P.longum
Linn P.mullesua Ham P.nigrum
Linn P.pseudonigrum Velayudhan P.schmidtii
Hook f. P.silentvalleyensis Ravindran P.sugandhi
Ravindran Babu P.trichostachyon
CDC P.wightii Miq
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P.longum-male
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P.hapnium
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P.mullesua
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P.schmidtii
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P.wightii
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Species diversity in NE Region
P.griffithi Cas DC P.muricatum var.glaberata
Griffith P.peepuloides Roxb P.betle
Linn P.boehmeriaefolium Wall.Cat P.hamiltonii
Cas DC P.aurantiacum Wall P.khasianum
Cas P.petiolatum Hook.f. P.chaba
H. P.sylvaticum Roxb P.thomsoni Hook
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P.chaba
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P.silvaticum
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EXOTIC COLLECTIONS
P.colubrinum
P.ornatum
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Cultivar diversity in black pepper
Aimpiriyan Arakkulammunda Balankotta Bilimalleges
ara Chengannurkodi Cheppakulamindi Cheriyakaniyak
adan Jeerakamundi Kalluvally Karimunda Kottan
Kottanadan Kutching Kurimalai Kuthiravali Kuttia
nikodi Malamundi Mallegesara Narayakodi Neelamu
ndi Nedumchola Neyyattinkaramundi Perambramunda P
erumkodi Poonjaranmunda Thommankodi Thevanmundi T
hulamundi Uddagara Vadakkan Valiyakaniyakkadan V
attamundi Vellanamban
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Black pepper germplasm conserved at IISR
Wild Accession 962
BP Cultivars 969
Karimunda accessions 200
Kottanadan accessions 68
Total 2199
Black pepper germplasm at AICRP-Spices Centers
Sl.No Centre Cultivated Wild Total
1 PRS, Panniyur 138 -- 138
2 PRS, Sirsi 75 21 96
3 RARS, Chintappally 26 29 55
4 HRS, Yercaud 106 -- 106
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Passport Details- Cultivars
View table
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DATA SHEET FOR WILD Piper
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Evaluation Data sheet- Cultivara
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