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DNA BARCODING RESEARCH IN INDIA :
EXCITEMENT AND DEVELOPMENT
Wazir S. Lakra*, M. Singh, M. Goswami,
A.Gopalkrishnan and S.Ayyappan
*Central Institute of Fisheries Education
(Indian Council of Agricultural Research )
Mumbai, India
Outline of the Presentation
Indian Biodiversity
Fish Diversity of India
Marine Diversity of India
Exotic Fish species in India
Institutional Capacity in Barcoding and Biodiversity
Research
FISH-BOL
Barcoding programs in India
Barcoding Training / Meeting / Workshop organized
Fellowships for Foreign Nationals for Barcoding
Research in India
Publications
Acknowledgement
Indian Biodiversity at a Glance
Major Groups No. of
species
% of World
species
Plants 45,523 11.80
Animals 89,492 7.28
Insects 59,353 6.83
Fishes 2,246 11.00
Amphibians 240 4.66
Reptiles 460 7.91
Birds 1,232 13.66
Mammals 397 8.58
Of the 34 biodiversity hotspots of the world, 3 are
located in India – the Western Ghats, North Eastern
Hills & Himalayas
Species Diversity of Indian Fishes
India has rich aquatic biodiversity spreading across different ecosystems
291 Exotic Fishes
2246
Freshwater
113 Brackish water
1368 Marine
No. of
Fish sp.
Ecosystem
765
Total
Important Fish Genetic Resources for Freshwater Aquaculture
•Indian major carps (4)
•Minor carps (9)
•Catfishes (13)
•Featherbacks (2)
•Snakeheads (8)
•Shads (1)
Chitala chitala
Ophiocephalus sp.
Pangasius pangasius
Labeo rohita
Catla catla
Cirrhinus mrigala
• Mullets
• Perches
• Chiclids
• Shads
Brackishwater Fish Genetic Resources
Tenualosa ilisha (Hilsa)
Chanos chanos
(Milk fish)
Lates calcarifer (Asian Seabass)
Mugil cephalus (Grey mullet)
Etroplus suratensis (Pearl spot)
Transition zone between
freshwater of the rivers and
saline water of seas
Salinity ranges from 0.5-30 ppt
Hoogly-Matlah, Mahanadi,
Godavari, Krishna, Cauvery
and large brackishwater lakes
such as Vembanad, Chilka and
Pulicat
Brackish water 1.24 million ha
Coldwater Fish Diversity
Mahseers: Tor sp.
Snow trouts : Schizothorax spp. Schizothoraichthys spp.
Loaches : Naemacheilus spp.
Minor carps: Labeo spp. Tor putitora
Labeo dero
Labeo dyocheilus
Schizothorax richardsonii Tor khudree
Himalayan rivers of Indus, Ganges and Brahmaputra River Basins.
Rivers originating and flowing through Western Ghats Krishna,
Cauveri, Bharatpuzha, Challakkudi, Periyar etc.
Temperature range subzero to 20 C.
Native Ornamental Fish Diversity of India
Freshwater Species ~ 280 species (mostly confined
to the Western Ghats & North-eastern Region).
Marine Ornamental Species ~ 170 species (mostly
from Lakshadweep & Andaman & Nicobar Species.
Name of the Group No. of
Species
Name of the Group No. of
Species
1. Plants Ctenophora 12
Seaweeds 131 Gastrotricha 98
Other Algae 593 Kinorhyncha 10
Sea grasses 14 Bryozoa (moss animals) 200
2. Animals Merostomata (Horse Shoe Crab) 02
2.1 Major phyla/Group - Invertebrates Pycnogonia 16
Protista (Protozoans) 750 Sipuncula 35
Porifera (Sponges) 486 Echiura 33
Cnidaria (Coelenterates) 842 Tardigrada (Water bears) 10
Nematoda ---- Phoronida 04
Platyhelminthes (Flat worms) 550 Chetognatha (arrow worms) 30
Annelida (Round worms) 440 2.3 Major phyla/Group - Vertebrates
Crustacea 2430 Protochordata (Urochordata &
Cephalochordata) 116
Mollusca 3370 Pisces (Marine & Brackishwater) 1474
Echinodermata 765 Reptiles (Sea Snakes & Sea Turtles)
26
Hemichordata (Prechordata) 12 Marine Mammals 29
2.2 Minor phyla/Group - Invertebrates Total 12490
Mesozoa 12
Marine Biodiversity of India
1,370 finfish species
Elasmobranchs
Sardines
Perches
Silverbellies
Carangids
Seerfishes
Ribbonfishes
Tunas
Arabian Sea, Bay of Bengal and Indian Ocean; surrounding east and west coasts of the main land and Lakshadweep, Andaman & Nicobar Islands
Coast line (Maritime States) : 8118 km
EEZ : 2 .02 million sq.km
Continental Self : 0.506 million .sq.km
Pomphrets
Shads
Sciaenids
Catfishes
Barracudas,
Red Mullets
Anchovies
Bulls-eye
Sharks
Pomphrets
Marine Fish Diversity
Shellfish Diversity
Crustaceans (Shrimps,Prawns,Crabs,
Lobsters) Total 2934 species
(95% marine) Nearly 350 species are commercially important 40 species have cultivable potential
Macrobrachium rosenbergii
Penaeus monodon
Scylla serata
Penaeus semisulcatus
Panulirus homarus
Thenus orientalis Penaeus indicus
Holothuria scabra
Echinoderms About 765 species are found in Indian marine waters. About 25 species are commercially important, popularly called as sea cucumbers.
Shellfishes Diversity
Starfish
Shellfishes Diversity
Mollusks
Nearly 5000 species species of mollusks found in Indian waters. Most of them are marine, few are estuarine and some others inhabit in freshwater ecosystem.
About 200 species like cuttle fish, squid, octopuses, oysters (pearl, edible), mussels, clams & marine ornamental gastropods are commercially important.
Sepia aculeata Perna viridis Pinctada fucata
New Fish Species Discovered From
•Western Ghats •NE India
Under ICAR-NATP- World Bank Project
• Over 50 percent of the world’s plant species and 42 percent of all terrestrial vertebrate species are endemic to the 34 biodiversity hotspots (Myers, 2000)
• Out of 34 across the world, 3 biodiversity hotspots are located in India
Western Ghats North Eastern Hills Himalayas
• Western Ghats along with Sri Lanka harbor 68% of freshwater fish species endemic to the Indian region alone
Biodiversity Hotspots
Alien fishes in India
Fresh water Food fish with less controversy
Cyprinus carpio cumminns Common carp
Cyprinus carpio specularis Mirror carp
Cyprinus carpio nudus Leather carp
Ctenopharyngodon idella Grass carp
Hypophthalmichthys molitrix Silver carp
Orechromis mossambicus Tilapia
Osphronemus gourami Gourami
Carassius carassius Golden carp
Puntius gonionotus Thai barb
Tinca tinca Tench
Onchorhynchus mykiss Rainbow trout
Salmo trutta fario Brown trout
Fresh Water Exotic Food Fishes not legally recognized
Aristichthys nobilis Bighead
Clarias gariepinus African catfish
Pangasius sutchi Thai pungas
Serrasalmus spilopleura Rupchanda, Paku
Oreochromis niloticus Nile Tilapia
Oreochromis zilli Red bellied tilapia
Oreochromis uroplepis Rufigi tilapia
Ictalurus punctatus Channel catfish
Mylopharyngodon piceus Black carp
Myliopharyngodon idella Mud carp
Exotic food fishes in India
83%
13%
4%
freshwater Marine shellfish
Sparus auratus Gilthead seabream
Pagrus major Red seabream
Dicentarchus labrax European seabream
Tranchinotus carolinus Florida pompano
Psedosciaena crocea Croceine croaker
Sciaenops ocellatus Red drum
Paralichthys olivaceus Bastard halibut
Exotic Shrimp Litopenaeus vannamei
Marine exotic fishes (introduced / in demand)
Popular Ornamental Exotic Fishes
Name of the fish Occurrence (%)
Goldfish (Carassius auratus) 100
Koi carp (Cyprinus carpio) 85
Siamese fighting fish (Betta spendens) 95
Penguin Fish (Thayeria obliqua ) 75
Mono Angel (Monodactylus argenteus) 75
Guppy (Lebistes reticulatus) 90
Gambusia (Gambusia affinis) 70
Swordtail (Xiphophorus helleri) 75
Oscar (Astronotus ocellatus) 75
Piranha (Serrasalmus sp.) 90
Arowana (Scleropages formosus) 90
Alligator gar (Lepisosteus sp.) 90
Indian Capacity in Biodiversity Research
ICAR / NARS (Ministry of Agriculture)
• National Bureau of Fish Genetic Resources, Lucknow
• National Bureau of Plant Genetic Resources, Delhi
• National Bureau of Animal Genetic Resources, Karnal
• National Bureau of Agriculturally Important Microorganisms, Mau
• National Bureau of Agriculturally important insects
Bangalore
• National Research Centre for Medicinal & Aromatic Plants, Anand
• 90 ICAR Institutes/Research Centers
• 50 Agricultural Universities
DAHD&F (Ministry of Agriculture)
• Fishery Survey of India, Mumbai
Indian Capacity in Biodiversity Research
CSIR/ DBT Institutes (Ministry of Science & Technology)
• National Botanical Research Institute, Lucknow
• Central Institute of Medicinal & Aromatic Plants, Lucknow
• Institute of Microbial Technology, Chandigarh
• Centre for Cellular & Molecular Biology, Hyderabad
• Laboratory for the Conservation of Endangered species (LACONES)
• National Institute of Oceanography, Goa
• Institute of Bioresources & Sustainable Development, Imphal
• National Centre for Cell Science, Pune
• Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum
Indian Capacity in Biodiversity Research
Ministry of Environment & Forests
• National Biodiversity Authority
• Zoological Survey of India
• Botanical Survey of India
• Forest Survey of India
• Indian Council of Forestry Research & Education
• Indian Institute of Forest Management
• Wildlife Institute of India
• Salim Ali Centre for Ornithology & Nat. History
Indian Capacity in Biodiversity Research
Miscellaneous Institutes/ NGOs/Universities
• Bombay Natural History Society
• Ashoka Trust for Research in Ecology and the
Environment
• M.S. Swaminathan Foundation
• Tata Energy Research Institute
• Universities having active Department of Life
Science/Zoology/Botany (>200)
Sequencing Facilities
• High-throughput 454 (Roche), Solid (ABI) & Illumina
whole genome facility (~ 10) * Govt. Institutions: NBRI, NBAIM, ICGEB, CCMB, NCCS, IGIB,
* Private Firms: Ocimum, Xcelars, Life Technologies, Bangalore
Genei
• Medium sequencing facility [48/96 Capillaries] (~75)
• Small sequencing facility [4-16 capillaries] (~200)
Indian Capacity in Biodiversity Research
• Plant Biodiversity :
NBPGR, NBRI, BSI, CIMAP, RGCB, NRCMAP, IARI,
FRI, SAUs
• Aquatic Biodiversity:
NBFGR, CMFRI, CIFE, CIFA, CIBA, CIFRI, NRCCWF,
FSI, NIO, BAMU, Fisheries Colleges / SAUs
• Animal Biodiversity:
WII, CCMB, (LACONES), NCCS, NBAIA, SACONH,
RGCB, SAUs
• Microbial Biodiversity: NBAIM, IMTECH, NIO, CIFT
Biodiversity Groups / Institutes (Sector – wise)
FISH-BOL: NBFGR and CIFE Work
• DNA Barcoding of Fish initiated at CIFE, Mumbai and NBFGR, Lucknow in 2005.
• Collected 3375 samples of 750 marine and freshwater species.
• Marine Fish Collection sites:
East & West Coast of India:
Mumbai, Cochin, Vishakhapatnam, Tuticorin & Mandapam.
Islands: Lakshadweep, Andaman & Nicobar.
Freshwater Fish Collection sites :
North-East, Western Ghats, Western Himalaya,
Manipur, Assam, Himachal Pradesh, Uttarakhand, Uttar Pradesh, Kerala, Tamilnadu, Karnataka, Maharashtra.
• DNA Barcodes generated : 2025.
Freshwater Fish
Marine Fish
Collection
of
Fish
Samples
from
Indian
Waters
Indian Marine Fish Barcoded
Order Family Genus Species
Perciformes
Clupeiformes
Mugiliformes
Siluriformes
Pleuronectiformes
Beloniformes
Aulopiformes
Major Groups: Carangids,
Clupeids, Scombrids,
Groupers, Sciaenids,
Silverbellies, Mullids,
Polynemids and Silurids
79 279
Indian Freshwater Fish Barcoded
Cypriniformes
Siluriformes
Perciformes
Synbranchiformes
Osteoglossiformes
Major Groups:
Cyprinids, Silurids,
Percids, Synbranchids and
Osteoglossids
50 84
Indian Ornamental Fish Barcoded
Covered under a separate
presentation
80
Summary of Genetic Divergence (K2P)
in Indian Marine Fishes
Taxa Min Dist (%) Max Dist (%)
Standard
Error
(SE)
Within Species 397 0.00 00.80 0.021
Within Genus 115 0.10 12.90 0.085
Within Family 79 0.20 23.10 0.032
Within Order 37 8.00 23.40 0.018
Within Class 6 13.20 24.30 0.007
Average Genetic Divergence Within Various
Taxonomic Levels in Marine Fishes
0
5
10
15
20
25
0.03
6.6
9.91 16.024.3
Taxa Min Dist (%) Max Dist (%)
Standard
Error
(SE)
Within Species 299 0.00 0.90 0.004
Within Genus 72 0.10 12.10 0.009
Within Family 50 0.80 18.00 0.012
Within Order 19 6.90
18.50 0.014
Within Class 5 8.10 21.10 0.015
Summary of Genetic Divergence
(K2P) in Indian Freshwater Fishes
Average Genetic Divergence Within Various
Taxonomic Levels in Freshwater Fishes
0
5
10
15
20
25
0.04
9.6
13.1 17.618.3
23.5 29.4
28.4
18.7
Average Nucleotide Frequences
Average Nucleotide Frequences
Summary of Average Nucleotide Frequencies
of Marine Fishes
Summary of Average Nucleotide
Frequencies of Freshwater Fishes
25
29.5 27.4
18
Average Nucleotide Frequencies
Average Nucleotide Frequencies
A T C G
Marine Fishes Freshwater Fishes
Summary
NJ
Tree
List of DNA Barcoded Marine Fish along with Genbank Accession No
List of DNA Barcoded Freshwater Fish along with Genbank Accession No
Forensic Application of DNA Barcoding in India
Identification of Endangered
Whale Shark (Rhincodon typus).
• Flesh, suspected as that of the Wildlife protected whale shark
(Rhincodon typus) seized from fishermen by the Forest Range
Officer (Govt. of Kerala), Kannur, Kerala.
• The Judicial First Class Magistrate, Thalassery, Kannur, Kerala
approached NBFGR for sample analysis and confirmation of
species (Case No. R.P.330/08, dt 29. 09. 2008).
• Based on DNA sequencing of COI (655bp), 16S rRNA(525bp) and
Cyt b(541bp) genes and comparing with the sequences earlier
generated by NBFGR (FJ375724, FJ375725, FJ375726) from a
stranded whale shark (from North Kerala, March, 2006), the
suspected sample was identified as that of endangered Whale
Shark (Rhincodon typus).
Forensic Application of DNA Barcoding in
India
Pomfret (Pampus chinensis) Identification –
cooked and raw fish.
1349A Pampus chinensis
Fried Sample(WL1)
1349B Pampus chinensis
Raw Sample(WL2)
Pampus chinensis Australia
Pampus argentius Australia
PA231B Pampus argentius
PA231C Pampus argentius
PA231D Pampus argentius
Parastromateus niger Australia
Parastromateus niger India
Thunnus albacares WL M457
100
28
20
100
100
95
100
85
95
NJ Tree of Pomfret Species found in India with cooked & raw
samples(WL1 & WL2).
Current Active Barcoding Programs in India
• DNA Barcoding fish and marine life (ICAR-NBFGR, CIFE):
Marathwada Uinversity, Pondichery University, Annamalai
University., CMLRE, RGCB .
• Barcoding Anurans of India (WII, University of Delhi).
• DNA Barcoding medicinal plants including Zingiberaceae:
Alpinia, Zingiber & Globba (RGCB & UoC).
• DNA Barcoding of Rattanas & Phyllanthus (UAS, BSI & ATREE).
• DNA Barcoding butterflies from Western Ghats (NCCS).
• DNA Barcoding insects-vectors, nematodes (VCRC- ICMR,
IISER, Kolkata
Current Active Barcoding Programs in India
• DNA Barcoding Dendrobium (DU & TBGRI).
• DNA Barcoding in Indian Taxa of Berberis (NBRI).
• DNA Barcoding in Bambusa species (TERI & TBGRI).
• Development of DNA Barcode for amphibian fauna of Western
Ghats (CEMDE & NCCS).
• Identification of Satyrine butterflies of Peninsular India through
DNA Barcodes (IISc & KFRI).
• DNA Barcoding of Dalbergia species (NBPGR, NCL & KFRI).
• HRD in DNA Barcoding at NBFGR, Lucknow and CIFE, Mumbai.
Government of India’s Existing Support to
Barcoding Research and Related Activities Organization Place Organism Approx. amount
National Bureau of Fish Genetics Resources (ICAR)
Lucknow Finfish & shellfish; Harmful algal bloom forming species
Rs. 15.0 Million +
Rs. 6.0 Million (HAB) Core funds- Rs. 40 Million
National Centre for DNA Barcoding, CIFE (ICAR)
Mumbai Fish & Marine Life Core funds (Rs. 30 Million)
National Bureau of Animal Genetics Resources (ICAR)
Karnal Cattle, goat, buffalo, yak, mithun, horse, camel, sheep, pig.
Rs. 20 Million
National Bureau of Plant Genetic Resources (ICAR)
New Delhi Plant species of economic importance; agricultural and horticultural crops.
Rs. 10.0 Million Core funds- Rs. 30 Million
National Bureau of Agriculturally Important Insects (ICAR)
Bangalore Agriculturally important insects Core funds- Rs. 25 Million
National Bureau of Agriculturally Important Microbes (ICAR)
Mau Agriculturally important microbes Core funds- Rs. 100 Million
Rajiv Gandhi Centre for Biotechnology in collaboration with University of Calicut and Kerala.
Trivandrum, Kerala Amphibians, Plants (Zingiberaceae- Alpinia, Zingiber & Globba), Marine molluscs.
Rs. 10.0 Million
Bharathiar University Coimbatore, TN Medicinal plant species of Apocynaceace and Zingiberaceae
Rs. 3.0 Million
Bharathidasan University Trichy, TN Grass species of the Western Ghats Rs. 4.0 Million
Organization Place Organism Approx. amount
Centre of Advanced Study in Marine Biology, Annamalai University
Parangipettai, TN Marine fishes of Parangipettai Rs. 4.0 Million
Pondicherry University (Department of Ocean Studies and Marine biology,
Port Blair Marine fishes of Andamans. Rs. 3.0 Million
University of Delhi and Wild life Institute of India
Delhi, Dehradun Indian amphibians Rs. 8.0 Million
Kerala Forest Research Institute jointly with Indian Institute of Sciences, Bangalore.
Trichur, Kerala Teak, Rose wood, Satyrine butterflies.
Rs. 7.0 Million
University of Delhi and Tropical Botanical Garden and Research Institute
Delhi, Trivandrum Dendrobium Species Rs. 4.0 Million
Centre for Marine Living Resources and Ecology
Cochin, Kerala Marine fishes of Indian EEZ. Rs. 30.0 Million
Indian Institute of Science Education and Research
Kolkata Nematodes Rs. 7.0 Million
National Botanical Research Institute
Lucknow Indian Taxa of Berberis Rs. 4.0 Million
Government of India’s Existing Support to
Barcoding Research and Related Activities
Organization Place Organism Approx. amount
Tropical Botanical Garden and Research Institute
Trivandrum, Kerala
Bambusa species Rs. 3.0 Million
UAS, Bangalore, Botanical Survey of India & ATREE
Bangalore Rattanas & Phyllanthus Rs. 2.7 Million BSI Core funds- 30 Million
Zoological Survey of India Kolkata Different animal taxa Core funds (Rs. 20 Million)
Vector Control Research Centre (Indian Council of Medical Research)
Pondicherry Insects-vectors Rs. 2.5 Million
Paul Hebert Centre for DNA Barcoding & Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University
Aurangabad Fishes Rs. 30 Million
Total Rs. 416.2 Million + other funds
Government of India’s Existing Support to
Barcoding Research and Related Activities
Trainings / Workshop / Seminar Organized
First International Training on DNA Barcoding of Marine Life at NBFGR,
Lucknow , April 16-21, 2007.
International Workshop on DNA Barcoding, 4 December, 2008 at NASC
New Delhi.
Short Course on DNA Barcoding Fishes and Marine Life at NBFGR,
Lucknow, December 3-12, 2009 .
International Consultation on DNA Barcoding, jointly organized by CIFE,
NBFGR, CBOL at NASC, New Delhi, 6-7 November, 2010.
First International Training on “DNA Barcoding of Marine
Life” at NBFGR, Lucknow, India, 2007
International Workshop on DNA Barcoding organized
by NBFGR & ABCS on 04 December 2008 at New Delhi
International Consultation on DNA Barcoding, jointly organized by CIFE, NBFGR,
CBOL at NASC, New Delhi, 6-7 November, 2010.
Fellowships for Doctoral and Post- Doctoral
Research in India for Researchers from
Developing and Other Countries
1. ICAR International Fellowship
Covers overseas candidates for study in the best Indian Agricultural
Universities in the ICAR-Aus System (NARS)
Duration : 3 years
Further Details : ICAR website “http://www.icar.org.in
2. TWAS Fellowship Program
TWAS-DBT Fellowship
TWAS-IACS Fellowship
TWAS-CSIR Fellowship
Duration : 6 months to 12 months
Further Details : www.twas.org
3. The African Scholarship Scheme
Masters and Doctoral Programmes
Duration : 2-3 years
Further Details :; www.aiuweb.org; www.ugc.ac.in; www.aicte.ernet.in
4. Commonwealth Scholarship
Graduate, Post-graduate and Doctoral programmes
Duration : 2-3 years
Further Details : http://www.ehow.com
Fellowships for Doctoral and Post- Doctoral
Research in India for Researchers from
Developing and Other Countries
Publication
Publication
Consortium of Barcode of Life (CBOL)
University of Adelaide
Indian Council of Agricultural Research (ICAR)
Local Organizers (Sally Brown)
Prof. Paul Hebert , Dr. R.D. Ward (Bob Ward)
Peter Freeman, Robert Hanner
All colleagues and students of Barcoding Team, India
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