Biodiversity Information in the Web with special reference
Biodiversity Information in the Web with special reference to spices Dr. Santhosh J. Eapen Bioinformatics Centre Indian Institute of Spices Research, Calicut-12
Beyond the specimen: genetic samples, field notes, images, recordings….
Biodiversity Data q The passport data management system ü handles basic information for each accession q The stock control system ü monitors incoming germplasm and the distribution of germplasm ü storage details of each accession q The evaluation data management system ü handles characterization data
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…. )
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
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
Major Databases Ú GRIN – USDA ARS (www. ars. usda. gov/npgs) Gateway to GRIN (Germplasm Resource Information System)Provides information about plants, animals, microbes and invertebrates Ú SINGER (System-wide Information Network for Genetic Resources) – CGIAR (www. singer. cgiar. org) Genetic resources collected and conserved by the CGIAR centers Ú Biotica – (http: //www. conabio. gob. mx) A Mexican biodiversity site for simple and reliable data capture of curatorial, nomenclatural, geographical and bibliographical data Ú BCIS – Biodiversity Conservation Information System (http: //www. biodiversity. org) Ú GBIF – Global Biodiversity Information Facility (http: //www. gbif. org) Ú Nature. Serve – a network site on conservation (http: //www. natureserve. org) Ú TOL - The Tree of Life (http: //tolweb. org)
Crop Based Databases • Barley Germplasm Database (www. grs. nig. ac. jp/barley) • 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)
Electronic Catalogues • Species 2000 (http: //www. sp 2000. org) • ITIS – Integrated Taxonomic Information System (http: //www. itis. usda. gov) • IPNI - The International Plant Names Index (http: //www. ipni. org)
Biodiversity Software • Bio. Link – 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)
Other Efforts • National Microbial Germplasm Project – USDA (www. ars. usda. gov/nmg) • MGD - Microbial Germplasm Database (www. mgd. nacse. org)
IISR Initiatives…… • SPICEGENES – Black Pepper – Turmeric – Nutmeg • PIR (Phytophthora Information Resource) • Piper. Base
Black Pepper Genetic Resources- A case study World Distribution of Piper Ø Central and South America (New world) Ø India, Malaysia, Indonesia and Sri Lanka (Old World) India: Two independent Centers 1. Western Ghats 2. North East Region
Indian Gene Centre: Present status • One of the 12 megadiversity centres • Two hot spots • Western Ghats • Northeastern Himalayas
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
Species Diversity of Piper in Western Ghats P. argyrophyllum Miq P. attenuatum Buch-Ham P. barberi Gamble P. betle Linn P. galeatum (miq) CDC P. hymenophyllum Miq P. hapnium Ham P. hookeri Miq P. longum Linn P. nigrum Linn P. schmidtii Hook f. P. sugandhi Ravindran & Babu P. trichostachyon CDC P. mullesua Ham P. pseudonigrum Velayudhan P. silentvalleyensis Ravindran P. wightii Miq
P. longum-male
P. hapnium
P. mullesua
P. schmidtii
P. wightii
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
P. chaba
P. silvaticum
ONS EXOT P. colubrinum P. ornatum IC ECTI L L O C
Cultivar diversity in black pepper Aimpiriyan Bilimallegesara Cheriyakaniyakadan Karimunda Kutching Kuttianikodi Narayakodi Neyyattinkaramundi Poonjaranmunda Thulamundi Valiyakaniyakkadan Arakkulammunda Chengannurkodi Jeerakamundi Kottan Kurimalai Malamundi Neelamundi Perambramunda Thommankodi Uddagara Vattamundi Balankotta Cheppakulamindi Kalluvally Kottanadan Kuthiravali Mallegesara Nedumchola Perumkodi Thevanmundi Vadakkan Vellanamban
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 1 Centre PRS, Panniyur Cultivated 138 Wild -- Total 138 2 PRS, Sirsi 75 21 96 3 RARS, Chintappally 26 29 55 4 HRS, Yercaud 106 -- 106
Passport Details- Cultivars View table
DATA SHEET FOR WILD Piper
Evaluation Data sheet- Cultivara
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