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Genomics-Introduction
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Beginners lessons in Genomics
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Genomics NotesIntroduction:
Genomics is an area within genetics that concerns the sequencing and analysis of an
organism’s genome. The genome is the entire DNA content that is present within one cell
of an organism. Experts in genomics strive to determine complete DNA sequences and
perform genetic mapping to help understand disease.
Genomics also involves the study of intragenomic processes such as epistasis, heterosis
and pleiotropy as well as the interactions between loci and alleles within the genome. The
fields of molecular biology and genetics are mainly concerned with the study of the role
and function of single genes, a major topic in today’s biomedical research. By contrast,
genomics does not involve single gene research unless the purpose is to understand a
single gene’s effects in context of the entire genome.
Genomics involves the study of all genes at the DNA, mRNA, and proteome level as well
as the cellular or tissue level.Genomics is a concept that was first developed by Fred
Sanger who first sequenced the complete genome of a virus and of a mitochondrion. He
initiated the practice of sequencing and genome mapping as well as developing
bioinformatics and data storage in the 1970s and 1980s.
The knowledge about genes that has so far been gathered has led to the emergence
of functional genomics, a field concerned with trying to understand the pattern of gene
expression, especially across different environmental conditions.
The term genomics was first coined in 1986 by Tom Roderick, a geneticist at the
Jackson Laboratory in Maine, during a meeting about the mapping of the human genome.
Physio-chemical properties of the genome:
The genome is the totality of the entire DNA of an individual or a species. It
includes all of the DNA, not just the genes. This definition is simple for the majority of
genomes, but all of the minor DNA components must also be considered.
For simple viruses, with a single nucleic acid molecule, the genome is obvious,
although of course for RNA viruses it is RNA rather than DNA. For haploid prokaryotes,
it is also straightforward, except for the plasmids, one copy of which is counted in the
genome. The genome of a species will be a representation of all the DNA (or RNA in
case of RNA viruses), to make up a typical genome for the individuals of that species.
For eukaryotes, one haploid copy of the DNA of each of the diploid pairs of
chromosomes (the autosomes) is included, plus one copy of the DNA of sex
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,chromosomes. Thus the female and male genomes will differ if the sex chromosomes are
different. One copy of the DNA from any organelles other than the nucleus, such as the
mitochondria and chloroplasts, should also be included; a complete list of such organelles
is probably not yet available for any species, but many are normally unimportant.
When the phrase “genome size” was first used to describe the total haploid DNA
content, there were strong objections, based on the concept that there is additional
information in the chromosomal proteins, and even in body structures, that is necessary to
propagate the lineage. While that point of view is not common at present, the proof has
not been made with eukaryotes that the DNA contains all of the information required for
maintenance of the lineage or species.
The majority of the DNA of a genome is not in the genes themselves and their
known associated regulatory sequence. While the phenomenon of gene regulation is
beginning to be understood, little is known of the significance of the majority of the DNA,
whether it has any functions other than acting as spacer between genes. In most species, a
large fraction of the DNA is repeated sequences that cause genetic recombination and
unequal crossing over, resulting in genomic rearrangements, but their overall significance
is not understood.
We think of the role of the genome as providing gene products, but in many
genomes only 1% or so of the DNA is transcribed and translated during normal cellular
activities. Striking evidence that the actual coding capacity is likely to be relatively
constant among plants is seen when comparing the genomes of Arabidopsis and maize.
Sequence information obtained from cDNAs indicates that both genomes code essentially
the same number of genes, although the genome sizes differ by two orders of magnitude.
Similarly, maize and sorghum are closely related plants that both have 10 chromosomes,
but the maize genome is more than three times the size of that of sorghum. When DNA
fragments from maize were used in hybridization analyses with sorghum sequences,
homology was shared predominantly by low copy number sequences and unique
sequences. In fact, several of the genes in sorghum show the same chromosomal
arrangement as their counterparts in maize. From these and similar analysis, the “extra”
DNA that accounts for the difference in maize and sorghum genome size apparently
comprises mostly non coding repetitive sequences between genes. This finding supports
the conclusion that the majority of nuclear DNA may play a supporting role in the
structure and organization of the genome but does not contribute directly to its protein-
coding capacity.
The size of the nuclear genome varies among organisms. The DNA content of
haploid eukaryotic cells (C value) ranges from 107 to 1011 bp. The human genome lies in
the middle of this range, at 3 X 109 bp. Although it has been assumed that organism
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, complexity correlates roughly with genome size – humans have larger genomes than
most insects, and insects have larger genomes than fungi- this correlation is by no means
universal. For example, some amphibians have genomes almost 50 times larger than that
of humans, and cartilaginous fish generally have larger genomes than bony fish.
Interestingly, genomes of plant are represented throughout the size range. The
smallest known plant genome of 7 X 107 bp belongs to Arabidopsis thaliana and one of
the largest is a member of the lily family, Fritillaria assyriaca, with 1 X 1011 bp. Rice,
maize and wheat fall in between these two, having genome sizes of 5 X 108, 6.6 X 109
and 1.6 X 1010 bp, respectively. The lack of a direct relationship between genome size
and organism complexity is called the C-value paradox. We have no satisfactory
explanation yet for the C-value paradox, but in plant, at least, we know that genome size
can to some degree be attributed to repetitive DNA and duplicated genomes (Polyploidy).
The field of genomics comprises structural genomics, which focuses on the
content and organization of genomic information, and functional genomics, which
attempts to understand the function of information in genomes. Comparative genomics
compares the content and organization of genomes of different organisms. Genomics
makes important contributions to human health, agriculture, biotechnology, and our
understanding of evolution.
Functional genomics:
Functional genomics is a field of molecular biology that attempts to make use of
the vast wealth of data produced by genomic projects (such as genome sequencing
projects) to describe gene (and protein) functions and interactions. Functional genomics
focuses on the dynamic aspects such as gene transcription, translation, and protein–
protein interactions, as opposed to the static aspects of the genomic information such as
DNA sequence or structures. Functional genomics attempts to answer questions about the
function of DNA at the levels of genes, RNA transcripts, and protein products. A key
characteristic of functional genomics studies is their genome-wide approach to these
questions, generally involving high-throughput methods rather than a more traditional
“gene-by-gene” approach.
A major branch of genomics is still concerned with sequencing the genomes of
various organisms, but the knowledge of full genomes has created the possibility for the
field of functional genomics, mainly concerned with patterns of gene expression during
various conditions. The most important tools here are microarrays and bioinformatics.
Methods for gene discovery
Need for gene discovery
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