Of the more than 30 species in the genus Radopholus, the burrowing nematode, Radopholus similis, is the only pathogen of widespread economic importance (Duncan and Moens, 2006). Radopholus similis is a migratory endoparasitic nematode that is known to be a destructive pest of citrus crops, pepper and, most importantly, banana, on which it causes toppling disease. The nematode causes economic problems throughout the world, most notably in warmer regions, including South America, the Caribbean, Africa, Asia and the Pacific.

1. AMIT KUMAR1, BASHAH JAVED2, TRIPTA KHARE3, ALOK KHARE4, D.K.GUPTA5
1. BIOTECHNOLOGY DEPTT., BAREILLY COLLEGE, BAREILLY
2. BIOINFORMATICS LAB, B.T.I., BAREILLY
3-4. ASSOCIATE PROFESSORS, BAREILLY COLLEGE, BAREILLY
5. H.O.D. BIOTECHNOLOGY, BAREILLY COLLEGE, BAREILLY.
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2. There are more than 30 species of Radopholus , but out of these only Radopholus similis is
the most widespread pathogen. This is the destructive pest for citrus crop, pepper and
mostly Banana.
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Its causes intensive destruction to root system
(preferring younger ones) of banana. Making
the plant to starve for water, nutrients and
lacking support.
Their infection is also supported by fungus and
other bacteria.
SYMPTOMS:
•Black lesions,
•Necrosis of root
•Stunted growth
•Yellowing of leaves
•Small fruit bunches
•Toppling in wind or rain
Acid fuschin-stained Radopholus similis in
infected roots

5. Males: Males do not resemble females
in appearance. They are 500-600
μm long and more slender than the females.
The head is rounded, non sclerotized
and offset by a conspicuous constriction
The stylet of the male is slender
and indistinct, 12 μm long, and has
small knobs which are difficult to
see.
Lip region is conical.
Long dorsal overlap.
Male has a bursa.
Tail tip is acute and rounded
Female: The female burrowing
nematode is 650-800 μm long and 20-24 μm
in diameter.
The head is rounded and slightly
flattened, offset by a slight constriction.
The stylet is about 18 μm long and has
prominent knobs.
The esophageal glands overlap the
intestine dorsally.
The vulva is located approximately 54%
of body length from the head.
There are two ovaries outstretched
anterior and posterior.
The spermatheca is spherical, usually
packed with rod-shaped sperm.
The tail shape is elongate conoid Ending
in a narrowly rounded terminus. The
posterior end of the tail has a
characteristic hyaline region.
Females and all the juvenile stages are infective whereas males are not infective.
 Females are hermaphrodite.
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6.  This burrows within the cortex
Whole lifecycle gets completed
within 20-25 days (at 24-32oC) or 18-20
days (at 24-27oC).
Lay 2eggs/day, either by sexual
reproduction with males or by
hermaphroditistim
 Hatching in 3-10days
Juvenile stage in 10-13 days.
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7. Longitudinal section of root infected
by Radopholus similis
Lesions and necrotic root induced by
feeding and tunneling
Uprooting of banana plant due to the severe damage caused by R.similis
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8. The Radopholus similis molecular studies have greatly simplified to
identify the effectors through transcriptome analysis.
The complete mitochondrial (mt) genome sequence of Radopholus
similis measures 16,791bp.
•Only 36 protein coding genes
•Can generate 5,853 ESTs
Any small mutation in any mitochondrial
Cytochrome subunits results in combined
complex defect.
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9. In NCBI the target sequence was identified from gene database with query
Rodopholus similis , in which the result there were 36 hits, out of which cytB
subunit III was isolated.
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10. The GenBank server provides full length information regarding the relevant species. It gives comprehensive
data that is publically available. This also contains links to other severs. The GenBank entries includes
description to the scientific name, taxonomy, features listing its biological significance.
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Raw nucleotide sequence from GenBank

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13. This identified FASTA sequence was uploaded to online protein modeling tool SWISS MODEL
for generating the 3-D structure of protein identified.
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15. The protein coding cytB B gene containing 340 amino acids [Chromosome MT - NC_013253.1] was
localized using NCBI, after which its translated sequence was subjected to the submission to
molecular modeling server. The resultant 3-D structure of protein was visualized on different
visualization softwares such as, SWISS-PDB viewer, RasMol, MDV.
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18. .Wire frame view of protein coded by cytB gene
. Ball and stick view of protein coded by cytB
gene
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Strand view of protein coded by cytB gene

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•Out of the 30 species of genus Radopholus,
the burrowing nematode, most important
species is the Radopholus similis.
•Its mitochondrial DNA contains exceptional
features correlated to DNA decoding.
• Therefore, in future this protein model can
be studied for its activity in performing
metabolic functions, detecting potent drug to
inhibit its function
•It will also be possible to identifying it’s
functional epitopes leading to vaccine
designing.

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