Practical No.

9
DATE :

OBJECTIVE
To retrieve the gene information of Arabidopsis thaliana for a particular condition using TAIR
database.

URL: https://www.arabidopsis.org/

Theory:
 Arabidopsis thaliana is a small flowering plant which belongs to the mustard family. Some special
characteristics of Arabidopsis thaliana, like small genome, very short life period, quick growth etc.
makes it a good genetic model organism. Since Arabidopsis thaliana is a model organism, most of
the researches are conducted using this plant. The Arabidopsis Information Resource (TAIR) is a
database which is an easy way to get a wide range of information about Arabidopsis thaliana. It
provides data including genes, gene product, gene expression, the complete genome sequences,
genetic markers, gene structure, physical markers, clones, mutants, metabolism, seed stocks,
genome maps, sequence polymorphism, research publications and about the research community.

Genome can be defined as the total content of genetic information in the chromosome of an

organism. Genome is made up of DNA. The aggregation of genes to form a long chain is called
chromosome. The small pieces of DNA or RNA in one unit of genome that can translate to protein
are called as gene. DNA (Deoxyribonucleic acid) is the genetic material that contains all the
information for the development and also maintains functions in living organisms. RNA is differing
from DNA only in 1 base pair i.e. in RNA it is uracil (U) instead of thymine. The genome
of Arabidopsis thaliana was completely sequenced in the year 2000. 

Since Arabidopsis thaliana has a small genome with five chromosomes, genetic manipulations are
easier making the plant useful for sequencing and genetic mapping. As one may know, sequencing
is the process of finding the amino acid sequence of protein whereas genetic mapping is the
process of making genome maps. Genome maps are the graphical representation of a gene on a
chromosome which gives information about its location. The plant has a very short life period. The
quick growth and small size of Arabidopsis thaliana makes it suitable for cultivation in
comparatively shorter time on a large scale. Arabidopsis thaliana  has a vital role in the transfer of
DNA in plant biotechnology. These characteristics of Arabidopsis thaliana make it a good genetic
model organism. The information about Arabidopsis thaliana would be very helpful for researchers
especially for researches in other flowering plants of same species. 

1
TAIR database
 
The Arabidopsis Information Resource (TAIR) is a database providing a wide range of information
about Arabidopsis thaliana. Arabidopsis thaliana  has been used as a model organism for research.
TAIR database provides data including genes, gene product, gene expression, the complete
genome sequences, genetic markers, gene structure, physical markers, clones, mutants,
metabolism, seed stocks, genome maps, sequence polymorphism, research publications and about
the research community.  
 Gene product can be either a protein or RNA (in non-protein coding genes) that is obtained from
the gene expression data. Gene expression is the process of producing the efficient protein or
RNA. The complete genome sequences is a process of finding an organism’s complete DNA. A
genetic marker can be defined as a DNA sequence or gene which has a known chromosome
location. The process of producing similar copies of organisms or cells or part of DNA is called
cloning and the outcome is called as a clone. A suddenly inheritable change in the genetic material
is called mutation. The resultant organism can be called as a mutant. All the chemical reactions in
a living organism, which accounts for the growth, are referred to as metabolism. Genome maps
are the graphical representation of a gene on a chromosome which gives information about its
location. The DNA sequence that derived from an mRNA is called as cDNA. ESTs or expression
sequence tag is a small section of a cDNA. Insertion of extra base pairs into DNA sequence is
called insertion mutations. Sequence polymorphism can be defined as the variation occurring in
the sequence among individual organisms. For example, the variation in single base pair in a DNA
sequence can be called as Single Nucleotide Polymorphism (SNP).
 The update of existing data with new information on the database is a continous process so as
ensuring most current info. TAIR is situated at the Carnegie Institution for Science Department of
Plant Biology, Stanford, California funded by the National Science Foundation. TAIR works in
partnership with Arabidopsis Biological Resource Center (ABRC) established at The Ohio State
University. Apart from the datasets, collection of seed, reproduction, preservation, distribution and
DNA resource are the biological materials provided to the research community by ABRC. The stock
search and order of ABRC is fully incorporated with TAIR. 
 TAIR stores the information about annotations on gene structure, gene / protein functional and
metabolic pathway.  Structural and functional annotation includes the recognition of gene
locations, coding regions and prediction of its function. Sequence of reactions that occur in an
organism for its development and survival is referred to as metabolic pathways.
 TAIR helps to get the information about an individual gene through its different tools. The main
tools are GBrowse, NBrowse, MapViewer, SeqViewer, the interaction viewer and Synteny viewer.
Data on multiple genes can be obtained by Bulk download tools and ftp files. GBrowse search or
browse the genes, cDNAs and ESTs, insertion mutants, SNPs, markers of Arabidopsis
thaliana  and was developed by Lincoln Stein. NBrowse is an interactive graphical browser used to
open Arabidopsis thaliana interaction network contains experimentally confirmed protein-protein
interactions. MapViewer is a tool which gives information about different sequence maps. A
graphical representation of the information can also be obtained from the tool. SeqViewer is a
genome browser. For a given short sequence or name, it will search for the possible hits in the
whole genome of Arabidopsis thaliana and give the result. It gives the information about the
annotation, transcripts, clones, markers on sequence of Arabidopsis. The Synteny Viewer is a tool
that compares and describes about the syntenic regions between genomes.

 
 

2
Procedure:
To retrieve the gene information of Arabidopsis thaliana for a particular condition using
TAIR database. 

Step 1: Open the URL: https://www.arabidopsis.org/

Step 2: In the search bar type what you want to know about A.thaliana.

Step 3: The database searches for the gene information that matching with the query term
you had typed in the text box

Step 4: Now we can select more accurate one from aal the given result.

3
RESULT

Fig 1: Homepage of TAIR

4
Fig 2: Search results for Stress Resistant Gene

Fig.3: Selected locus giving more details.

5
6