This document provides an overview of genomics and related fields. It discusses the historical discoveries that laid the foundations of genomics. It then defines key genomics terms and describes different areas of genomics research like comparative genomics, metagenomics, structural genomics, functional genomics, transcriptomics, proteomics and metabolomics. The document also discusses genome sequencing techniques, genome organization of different organisms like bacteria, plants and humans. It concludes with an overview of genome mapping methods.

2. manju s s

3. Contents
• Genomics – Introduction
• Other “Omics”
• Genome Sequencing
• Genome Organization
• Genome Mapping

4. Historical Background
• 1868 : Miescher – Discovered DNA
• 1944 : Avery – DNA as genetic material
• 1953 : Watson & Crick – Double helical structure of DNA
• 1965 : Holley – Sequenced yeast tRNA for Alanine
• 1970 : Wu – Sequenced Lambda cohesive end DNA
• 1977 : Sanger – Developed dideoxy termination method
: Gilbert – Developed chemical degradation method
• 1980 : Messing – Developed M13 cloning vectors
• 1986 : Hood – Developed partially automated sequencing
And many more.

5. INTRODUCTION
• “Genome” refers to one complete set of
chromosomes or DNA in an organism.
• “Genomics”, a term coined by Thomas
Rodrick in 1986.
• Genetics subdiscipline of mapping,
sequencing and analyzing the functions
of entire genome.
• Publically funded Human Genome
Project, launched in 1990.
• Genomics era – 1995 (First complete
genome sequence of Hemophilus
influenzae).

6. Classification of Genomics

7. • Comparative genomics: The genomic features of
different organisms are compared to study basic biological
similarities and differences as well as evolutionary
relationships between organisms.
• Metagenomics: The study of genetic material recovered
directly from environmental samples. For ex: To analyze
microbes without culturing them in the laboratory, using PCR
and modern DNA analysis techniques.

8. Structural Genomics
• Describes the 3D structure of
every macromolecule specially
emphasizing on every protein
encoded by a given genome.
• It attempts to determine the
structure of every protein
encoded by the genome, rather
than focusing on one particular
protein.
• It takes the advantage of
completed genome sequences
in several ways.

9. Methods
1. De nova methods: Proteins are purified and crystallized and then
subjected to X-ray crystallography and NMR.
2. Modeling – based methods
a. ab initio modeling: It uses protein sequence data and the
chemical and physical interactions of the encoded amino acids to predict
the 3D structures of proteins with no homology to solved protein structure.
b. Sequence–based modeling: Compares the gene sequence of an
unknown protein with sequence of proteins with known structures.
Depending on the degree of similarity between the known protein structure
and the unknown protein the structure of unknown protein is identified.
c. Threading: It is based on fold similarities rather than sequence
identity. Identify distantly related proteins and can be used to infer
molecular functions.

10. Functional Genomics
• Understanding the activity of
the genome as a whole.
• Assigns functions to the
products of genes.
• Functional Genomics gives
rise to other “Omics”
 RNAomics
 Transcriptomics
 Proteomics &
 Metabolomics

12. RNAomics
DNA RNA
• RNA an important biomolecule having double role.
• Thomas .R. Cech discovered its dual role
as Catalyst as Regulatory system
• RNA – its secondary structures, discovery of non-coding
RNAs, its classification and RNA-interference (RNAi) are
studied under RNAomics.

13. Transcriptomics
Gene mRNA
• Full complement of mRNA molecules produced by the
genome has been termed the “Transcriptome”.
• Human – only 3% of the genome is represented by genes.
• But transcriptome is much more than just the transcribed
portion of the genome.
• Alternative splicing and RNA editing increases the complexity
of transcriptome by each gene potentially giving rise to many
transcripts.
• One Gene thousands or millions of distinct
transcripts.

15. Transcriptomics
• All genes are not expressed simultaneously, in the same tissue, at the same
level.
• Transcriptomics looks at the steady-state mRNA level and rate of RNA
turnover.
• Transcriptomics techniques identifies mRNA by comparing relative
abundances with in and / or between the samples.
Approaches:
1. Direct sampling of mRNA sequences
a) cDNA library: Converting mRNA into cDNA library. Comparisons
between the cDNA sequences and the genome sequences will reveal the
identities of the genes whose mRNAs are present in the transcriptome.
b) Serial Analysis of Gene Expression (SAGE): It yields about 12 bps
short sequences, each of which represents an mRNA present in the
transcriptome. These short sequences are sufficient to enable the gene that
codes for the mRNA to be identified.

16. 2. Hybridization analysis
a) Microarray: It enables more accurate comparisons of the amounts of
individual mRNAs giving relative abundances.
Steps:
Every gene in a given sample is spotted
mRNA is extracted under a particular condition
Converted to cDNA
Labeled cDNA is hybridized on to the spotted gene.
Signals generated indicates the active genes under a given condition.
b) DNA chips: Thin wafers of silicon carrying different oligonucleotides
synthesized directly on the surface of the chip.
Each oligonucleotides are specific for different gene present in a sample
and are relatively easy to prepare.
Hybridization between an oligonucleotide and the probe is detected
electronically.

17. Proteomics
• Transcriptome gives an accurate
indication of genes that are active in
a particular cell but not the proteins
that are present.
• “Proteome” is the entire collection
of proteins in a cell, tissue or
organism at a certain time.
• Proteomics is large scale study of
proteins.
• The factors that influence protein
content include not only the amount
of each mRNA that is available, but
also the rate at which an mRNA is
translated into protein and the rate at
which the protein is degraded.
• Protein profiling methods:
1. Protein electrophoresis
2. Mass spectrometry

18. Metabolomics
• Many proteins are enzymes.
• The metabolome is the quantitative
description of all of the small
molecules in a cell or organism.
• 1. Primary metabolites &
2. Secondary metabolites
• Metabolic pathways never exist in
isolation but are part of much
larger networks.
• The goal of metabolomics is the
unbiased identification and
quantification of all the metabolites
present in a sample taken from an
organism.

19. • Metabolite analysis:
a. GC and HPLC – to separate molecules.
b. MS and NMR – to identify the chemical components.
• Applications:
1.Disease diagnosis
2.Plant biologists are far ahead in studying metabolomics, thousands of
secondary metabolites have been identified in plants.

20. Human metabolomics studies are different
from other organisms
• Human populations are outbred.
• Differing in diets from individual to individual.
• Taking drugs.
• Role of gut microflora.

21. Genome Sequencing not Gene sequencing
• Existing sequencing technology could be used if the large genome could be
broken down into more manageable pieces and then joining of these pieces
can be accomplished using larger, overlapping fragments.
• Determining the order of bases, identified by the letters A,C,G and T along
the DNA molecule.
• Basic Procedure:
Fragmentation of the genome
Cloning of each fragment
Sequencing each fragment
Rejoining the fragments using large overlapping sequences.

22. Types
• Hierarchical Sequencing
• Shot-gun Sequencing
• Clone-contig Sequencing
• High-throughput Sequencing

25. High-throughput sequencing

26. Genome Organization
 DNA of an organism is composed of an array of arrangement of four
nucleotides in a specific pattern.
 Genome when seen from viewpoint of sequences of these nucleotides
alone, is like a book which doesn't have any chapters or paragraphs or even
sentences. Hence, these nucleotides conceal a layer of unapparent
information.
 Genomic organization of an organism is this background layer of
information which unassumingly provides multiple layer of information to
structure genome from the array of nucleotide sequences.
 A number of major differences have emerged between eukaryotic and
prokaryotic genomes.
 Model organisms
 Easy to grow and study in laboratory
 Their genetics are well studied
 Exhibit characteristics that represent a larger group of organisms.

27. Bacterial genome-E.coli
• 4288 putative protein coding
genes
• 1/3 rd of which are well studied
genes encoding known
proteins.
• 38% are of unknown function.
• Average distance between
genes is 118bp.
• Sequence comparisons can
often be used to gain inferences
about gene function.

28. Plant genome- Arabidopsis thaliana
• Small genome – 125mb
• Near absence of interspersed repetitive
DNA
• First plant to have its genome sequenced
• 28,000 protein coding genes but,
remarkably many of these genes are
duplicates and probably originated by
chromosomal rearrangements, hence only
15,000 unique genes are left.
• Many genes found in fruit flies and
nematodes have homologs with
Arabidopsis and other plants, suggesting
plants and animals have common ancestors.

29. Cereal genome-Rice
• Cereal crops provide much of
food for humans and their
domestic livestock.
• Rice – 2n=24 Chromosomes,
430mb (smallest genome).
• Conserved genome structure
among other cereal grasses
assist plant breeders.
• A genome wide survey of
interactive genetic loci has
identified various reproductive
barriers that may drive
speciation of the rice genome.

30. Human genome
• First Human genome
sequence was completed by
2003.
• Surprises in Human genome
 Only 2-3% of total genome
codes for protein.
 Variation in gene size is
about 1000 to 2.4 million bp.
 50% of the genome is made
up of transposons and other
highly repetitive sequences.
 97% of the genome is the
same in all people.
 7 million SNPs in humans.

31. Applications of Human genome
• Complex phenotypes are
determined by multiple
genes interactions with
environment.
• Understand the genetic
basis of certain diseases
• Identifying SNPs.
• Pharmacogenomics and
Personalized medicine.

32. Genome Mapping
• Helps to identify and isolate genes
based of an information about their
location in the genome.
• Maps can be used as a scaffold to
assemble the sequence.
• DNA probes to identify
polymorphic sequences.
• Different types of maps:
1. Genetic maps- SNPs, RFLPs,
STRs
2. Cytological maps- Chromosome
staining (Q-banding Quinacrine, G-
banding Giemsa stain) and FISH
3. Physical maps – Directly locates
the positions of specific sequences
on chromosome

33. Genome Mapping
1. Genetic Maps: the process of determining the order of and relative distance
between genetic markers (specific sequences or heritable elements that
generate a phenotype) on a chromosome based on their pattern of inheritance.
2. Cytological Maps: a graphic representation of the location of genes on a
chromosome, based on correlating the genetic recombination results of
testcrosses with the structural analysis of chromosomes that have undergone
changes, such as deletions or translocations, as detected by banding
techniques.
3. Physical Maps: provide specified detail about the number of bases and
physical distance that exists between genetic markers.
a) Radiation hybrid mapping is a method used to construct physical maps that
uses radiation or x-rays to break DNA into fragments to determine the
distance between genetic markers and their order on the chromosome.
b) Sequence mapping is a method used to construct physical maps that uses
already-known locations of genetic markers to determine distances in number
of base pairs.
• Expressed sequence tag (EST): a short sub-sequence of a cDNA sequence
that may be used to identify gene transcripts.

34. References
• Life – The Science of Biology, David Sadava et al; W.H.
Freeman Publisher, 9th
Ed, (2010).
• Principles of Gene Manipulation and Genomics, S.B. Primrose
and R.M. Twyman, Blackwell Publishing, 7th
Ed, (2006).
• Genomes 3, T.A. Brown, Garland Science Publishing, 3rd
Ed,
(2007).
• Principles of Genetics, Snustad and Simmons, 3rd
Ed, (2003).
• ISAAA Resources, Pocket K No. 15: ‘Omics' Sciences:
Genomics, Proteomics, and Metabolomics.
• Structural and functional analysis of rice genome, Akhilesh K.
Tyagi et al; J. Genet. Vol 83, 79-99,(2004).