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    Experiment No.1

    Aim: To study the plant genome organization and evolution ofArabidopsis thaliana.


    The plant genome organization describes the genomic size, chromosome number, repeatsequences, how the genes are organized etc. For the genome organization and evolution the

    NCBI Databases & Tools are used. NCBI is used to predict the genome organization of any

    plant genome.


    Arabidopsis was the first plant genome to be sequenced, and is a popular tool for

    understanding the molecular biology of many plant traits, including flower development

    and light sensing.Arabidopsis thaliana(A-ra-bi-dp-sis tha-li--na; thale cress, mouse-ear

    cress or arabidopsis) is a small flowering plant and is a popular model organism in plant

    biology and genetics. The advanced fields of bioinformatics and biotechnology have changedthis paradigm, enabling the analysis of organisms in terms of genome organization,

    expression and interaction. The study of the way genes and genetic information are organized

    within the genome, the methods of collecting and analyzing this information and how this

    organization determines their biological functionality is referred to as genomics. Genomic

    approaches are permeating every aspect of plant biology, and since they rely on DNA-coded

    information, they expand molecular analyses from a single to a multispecies level. Plant

    genomics is reversing the previous paradigm of identifying genes behind biological functions

    and instead focuses on finding biological functions behind genes. It also reduces the gap

    between phenotype and genotype and helps to comprehend not only the isolated effect of a

    gene, but also the way its genetic context and the genetic networks it interacts with can

    modulate its activity.


    Plant: Arabidopsis thaliana

    Database: NCBI


    The genome organization and evolution is predicted by the following steps.

    Open the Genome resource from the NCBIresources(

    From the custom resources of Genome select the Plant resource.

    Select the plant Arabidopsis thaliana.

    It will provide the genome organization of Arabidopsis thaliana.


    Genome Resource
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    Plant Resource:

    Genome Organization and Evolution:

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    Arabidopsis thaliana is a small flowering plant of mustard family, brassicaceae (Cruciferae).

    It is distributed throughout the world and was first reported in the sixteenth century by

    Johannes Thal. It has been used for over fifty years to study plant mutations and for classical

    genetic analysis. It is now being used as a model organism to study different aspects of plant


    Arabidopsis thaliana is a diploid plant with 2n = 10 chromosomes. It became the first plantgenome to be fully sequenced based on the fact that it has a (1) small genome of ~120 Mb

    with a simple structure having few repeated sequences (2) short generation time of six weeks

    from seed germination to seed set, and (3) produces large number of seeds. The sequencing

    was done by an international collaboration collectively termed the Arabidopsis Genome

    Initiative (AGI). Though of no economic importance, it is an invaluable resource to

    agriculturally important crops, particularly to members of the same family, which includes

    canola, an important source of vegetable oil.

    Genome Assembly and Annotation:

    Assembly and Annotation

    Default assembly

    1 other assemblies are availableAssembly Name TAIR9

    Last sequence update 19-Jun-2009

    Highest level of assembly complete sequence genome

    Size (total bases) 119,146,348

    Number of genes 33,323

    Number of proteins 35,176

    Mitochondrial Genome

    Last record update 31-Jul-2008Last sequence update 12-Dec-2002Size 366,924Number of genes 131

    Number of proteins 117Chloroplast Genome Pltd

    Last record update 26-Mar-2010Last sequence update 07-Apr-2000Size 154,478Number of genes 129Number of proteins 85

    Arabidopsis thaliana
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    The Arabidopsis Information Resource (TAIR)Arabidopsis assembly project

    Loc Type


    me RefSeq INSDC


    (Mb) GC% protein rrna trna


    rna gene pseudogene

    Nuc Chr 1 NC_003070.9 CP002684.1 30.43 35.9 9,263 - 240 218 8,433 924

    Nuc Chr 2 NC_003071.7 CP002685.1 19.7 35.9 5,560 2 96 149 5,513 1,043

    Nuc Chr 3 NC_003074.8 CP002686.1 23.46 36.3 6,908 2 93 134 6,730 1,080

    Nuc Chr 4 NC_003075.7 CP002687.1 18.59 36.2 5,356 - 79 116 5,140 832

    Nuc Chr 5 NC_003076.8 CP002688.1 26.98 35.9 8,089 - 123 127 7,507 948

    MT Chr MT NC_001284.2 Y08501.2 0.37 44.8 117 3 21 - 131 -

    Chl Chr Pltd NC_000932.1 AP000423.1 0.15 36.3 85 7 37 - 129 -

    Arabidopsis thaliana

    Arabidopsis Genome InitiativeArabidopsis thaliana legacy genome sequence



    e Name


    q INSDC












    rna gene





    Chr 3 - BA000014.


    23.4 36.


    5,228 31 92 6 4,40





    Chr 5 - BA000015.


    23.81 36.


    4,710 - 107 10 1,83





    Chr 1



    - AE005173.


    14.67 35.


    3,140 - 128 - 2,71





    Chr 1 top


    - AE005172.


    14.22 36.


    3,323 1 78 1 2,35





    Chr 4 long


    - AJ270060.


    14.5 36.


    3,156 - 55 - 4,72





    Chr 4 short


    - AJ270058.


    3.05 36.


    554 - 8 - 817 -
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    The genome organization and evolution ofArabiopsis thaliana was successfully studied. I

    found thatArabidopsis thaliana is a small flowering plant of mustard family having 10chromosomes with ~ 120 Mb genome size.

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    Experiment No. 2

    Aim of the experiment:

    To identify gene in Arabidopsis thaliana for transgenic approach in plants

    Principle: For the identification of the genes in Arabidopsis thaliana I have used the


    Chemgenome is an ab-intio gene prediction software, which find genes in prokaryotic

    genomes in all six reading frames. The methodology follows a physico-chemical approach

    and has been validated on 372 prokaryotic genomes. Read more about ChemGenome


    Genome: Arabidopsis thaliana chromosome1

    Tool: ChemGenome 2.0


    1. A Physico-Chemical model for analyzing DNA sequences", Dutta S., Singhal P.,Agrawal P., Tomer R., Kritee, Khurana E. and Jayaram B., J. Chem. Inf. Mod., 2006,

    46(1), 78-85.

    2. "Decoding the design principles of amino acids and the chemical logic of proteinsequences", Jayaram B., Nature Precedings, 2008.
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    Principle Outcome:


    We have successfully identifed gene in Arabidopsis thaliana which can be transferred from

    one plant to another.

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    Experiment No. 3

    Aim: To study plant metabolic pathway inArabidopsis thaliana.


    Metabolic pathways are series ofchemical reactions occurring within a cell. In each pathway,a principal chemical is modified by a series ofchemical reactions. For the metabolic pathway

    analysis the AraCyc database is used

    Method Specification:

    Database: AraCyc (BioCyc)


    1. Glycolysis

    2. Pentose phosphate pathway3. Photorespiration

    Principle Outcome:

    1. Glycolysis

    The pathway starts with-D-glucose-6-phosphate, made from starch degradation. The first

    committed step of glycolysis is the reversible conversion of-D-glucose-6-phosphate into D-

    fructose-6-phosphate by hexose phosphate isomerase, which changes the pyranose

    configuration of glucose into the furanose configuration of fructose. The second step is

    catalyzed by a phosphofructokinase in the presence ofATP; this step is irreversible. The third

    step is catalyzed by an aldolase which cleaves fructose-1,6-bisphosphate into interconvertable
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    two three-carbon fragments: D-glyceraldehyde-3-phosphate and dihydroxyacetone

    phosphate. The interconversion of these tautomers is facilitated by a triose phosphate

    isomerase. The following reaction, which adds one phosphate residue to D-glyceraldehyde-3-

    phosphate to form 1,3-diphosphateglycerate , is freely reversible and

    requires NAD+

    and phosphate . The next step releases one molecule of ATP during the

    conversion of1,3-diphosphateglycerate into 3-phosphoglycerate by a Mg2+

    -dependentglyceraldehyde-3-phosphate kinase. The next step requires little energy change and leads to

    the reversible transfer of a phosphate group from the 3- to the 2-hydroxyl group of glycerate,

    leading to the formation of2-phosphoglycerate . The removal of a molecule of water by an

    enolase in the presence of Mg2+

    converts 2-

    phosphoglycerate into phosphoenolpyruvate (PEP). The final step of glycolysis involves the

    ketolization of PEP to pyruvate by a pyruvate kinase, leading to the release of a molecule of

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    2. PhotorespirationThe first step of the pathway involves the dephosphorylation of2-phosphoglycolate, In its

    dephosphorylated form glycolate is exported to the cytoplasm where it is oxidized in the

    peroxisomes to glyoxylate . The H2O2 generated during this step is detoxified by catalases in

    the peroxisome. Glyoxylate is then converted into glycine by two different enzymes:

    serine:glyoxylate aminotransferase and glutamate: glyoxylate aminotransferase. Glycine is infact converted into serine in the mitochondrion by glycine decarboxylase where it is

    extremely abundant. Glycine decarboxylase has four different subunit (P, H, T and L), which

    catalyze the transfer of a methylene group from glycine to tetrahydrofolate with the

    concomitant release of NH3 and CO2, and production of NADH. The methylene group is then

    transferred to another glycine molecule to form serine by a serine hydroxylmetyltransferase.

    Back in the peroxisome, serine is used to convert glyoxylate into hydroxypyruvate via

    serine:glyoxylate aminotransferase as mentioned above. The last of the peroxisome steps

    consists in the reduction of hydroxypyruvate into glycerate by an NADH-dependent

    hydroxypyruvate reductase. Glycerate is then redirected to the chloroplast where it is

    phosphorylated to 3-phosphoglycerate and reenters the Calvin cycle
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    3. Pentose phosphate pathwayThe pentose phosphate pathway is an alternative way of oxidizing glucose. This oxidation is

    coupled with NADPH synthesis. The pathway has two primary reaction sequences:

    the pentose phosphate pathway (oxidative branch) and the pentose phosphate pathway (non-

    oxidative branch). In the former,-D-glucose-6-phosphate is oxidized to D-ribulose-5-

    phosphate0; this step is the source of reducing equivalents for biosynthesis reactions in theshape ofNADPH. The subsequent non-oxidative portion represents a series of transaldolase

    and transketolase reactions, in which D-ribulose-5-phosphate is converted into D-fructose-6-

    phosphate and D-glyceraldehyde-3-phosphate. As a result this pathway is a source of

    reducing power and is also important for the conversion of hexoses to pentoses


    We have successfully studied the above three pathways in Arabidopsis thaliana from theAraCyc (BioCyc) pathway database.
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    Experiment No. 4

    Aim: To comparatively study the plant genomes.

    Principle:Comparative genomics, the study of the similarities and differences in structureand function of hereditary information across taxa, uses molecular tools to investigate manynotions that long preceded identification of DNA as the hereditary molecule. In most plants,

    the evolution of the small but essential portion of the genome that actually encodes the

    organism's genes has proceeded relatively slowly; as a result, taxa that have been

    reproductively isolated for millions of years have retained recognizable intragenic DNA

    sequences as well as similar arrangements of genes along the chromosomes.

    Method Specification:

    Tool: BioEdit

    Plants:1. Arabidopsis thaliana(Model Plant)

    >gi|281199944|gb|GU223224.1| Pisum sativum sulfiredoxin precursor protein

    (Srx) gene, complete cds







    2. Pisum sativum (Target Plant)

    >gi|326937563|emb|FN691474.1| Arabidopsis thaliana sph6 gene for S Protein

    Homologue 6









    1. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor andanalysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41:95-98.

    Principle Outcomes:DNA molecule: arabidpsis thaliana

    Length = 453 base pairsMolecular Weight = 136212 Daltons, single stranded

    Molecular Weight = 273979 Daltons, double stranded

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    G+C content = 31.35%

    A+T content = 68.65%

    Nucleotide Number Mol%

    A 150 33.11

    C 55 12.14

    G 87 19.21

    T 161 35.54

    DNA molecule: pisum sativum

    Length = 390 base pairs

    Molecular Weight = 118241 Daltons, single stranded

    Molecular Weight = 237117 Daltons, double stranded

    G+C content = 50.00%

    A+T content = 50.00%

    Nucleotide Number Mol%

    A 108 27.69

    C 83 21.28

    G 112 28.72

    T 87 22.31

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    Pairwise Alignment:

    Sequence 1: arabidpsis thaliana

    Sequence 2: pisum sativum

    Optimal Global aligment

    Alignment score: 84

    Identities: 0.43

    Conclusion: We have successfully compared two plant nucleotide sequences from

    Arabidopsis thaliana and Pisum sativum, we found that the both sequences are 43% identical.

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    Experiment No.5

    Aim: To identify the Drug targets in plants.


    Molecular modelling encompasses all theoretical methods and computational techniquesused to model or mimic the behaviour ofmolecules. The common feature of molecular

    modelling techniques is the atomistic level description of the molecular systems; the lowest

    level of information is individual atoms

    Docking is a method which predicts the preferred orientation of one molecule to a second

    when bound to each other to form a stable complex. Docking is frequently used to predict the

    binding orientation ofsmall molecule drug candidates to their protein targets in order to in

    turn predict the affinity and activity of the small molecule.

    Method Specification:

    Receptor: 3O74

    Ligand: 2XZP

    Tool: HEX6.3

    Reference: Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coled Coils from

    Protein Sequences, Science 252:1162-1164
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    Principle Outcome:

    Conclusion:We have successfully identified ligand drug target 2XZP for receptor 3O74 of Pseudomonas

    putida as it shows maximum binding affinity in Docking

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    Experiment No.6

    Aim: To design plant nucleotide primer using primer designing tool.


    A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. Theyare required for DNA replication because the enzymes that catalyze this process, DNA

    polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase

    starts replication at the 3'-end of the primer, and copies the opposite strand.

    In most cases of natural DNA replication, the primer for DNA synthesis and replication is a

    short strand of RNA

    Method Specification:

    Sequence: Arabidopsis thaliana actin 3 gene, complete cds. GenBank: U39480.1

    Tool: Geneious Pro 5.3.5


    Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J,

    Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2011)

    Geneious v5.4, Available from

    Principle Outcome:
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    Type Name Sequence Minimum Maximum Length #



    primer_bind 1st forwardprimer

    TGAGCAGGAGCTTGAGACGGC 2501 2521 21 1 forward

    primer_bind 2nd forwardprimer

    GCCTTAACCGAGGCCGAGCG 848 867 20 1 forward

    primer_bind 3rd forward


    GCCTTAACCGAGGCCGAGCG 848 867 20 1 forward

    primer_bind 4th forward


    GCCTTAACCGAGGCCGAGCG 848 867 20 1 forward

    primer_bind 5th forward


    GCCTTAACCGAGGCCGAGCG 848 867 20 1 forward

    primer_bind_reverse 1st reverse


    ACCTCAGGGCAACGGAAACGC 2591 2611 21 1 reverse

    primer_bind_reverse 2nd reverseprimer

    GCTTCGAATTCGGCACACCTCGT 933 955 23 1 reverse

    primer_bind_reverse 3rd reverse


    GCTTCGAATTCGGCACACCTCG 934 955 22 1 reverse

    primer_bind_reverse 4th reverse


    GGCTTCGAATTCGGCACACCT 936 956 21 1 reverse

    primer_bind_reverse 5th reverse


    AGGCTTCGAATTCGGCACACC 937 957 21 1 reverse


    We have successfully designed primers for Arabidopsis thaliana actin 3 gene, complete cds

    sequence using primer designing tool Geneious Pro 5.3.5

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    Experiment No.7

    Aim: To draw phylogram using different plant protein sequence.

    Principle: Phylogenetic methods can be used for many purposes, including analysis of

    morphological and several kinds of molecular data.

    Method specification:

    Plants:1. oryza sativa2. Pseudoterranova decipiens and3. solanum tuberosum

    Tool: Geneious 5.1.7

    Principle Outcomes:

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    + oryza sativa



    ========================= Pseudoterranova decipiens

    |+=============================== solanum tuberosum

    In Newick format:

    ('oryza sativa':0.0,'Pseudoterranova decipiens':1.242189,'solanum


    Conclusion: we have successfully drawn phylogram using plant protein sequences of oryza

    sativa, Pseudoterranova decipiens and solanum tuberosum

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    Experiment No.8

    Aim: To identify the secondary metabolites as drug targets for diseases in plants.


    Secondary metabolites are organic compounds that are not directly involved in thenormal growth, development, or reproduction of an organism. Secondary metabolites often

    play an important role in plant defense against herbivory and other interspecies defenses.

    Plants use secondary metabolites as medicines, flavorings, and recreational drugs. Secondary

    metabolites are essentially low molecular weight compounds, sometimes having complex

    structures. They function in processes as diverse as immunity, anti-herbivory, pollinator

    attraction, communication between plants, maintaining symbiotic associations with soil flora,

    enhancing the rate of fertilization etc., and hence are significant from the evo-devo


    Method Specification:

    Receptor: 2XAM (Plant Hydrocarbon)

    Ligand: 2XAL

    Tool: HEX6.3

    Reference: Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coled Coils from

    Protein Sequences, Science 252:1162-1164

    Principle Outcome:
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    We have successfully identified ligand drug target 2XZP for receptor 3O74 of Pseudomonasputida as it shows maximum binding affinity in Docking using HEX6.3.