Comparative genomics involves comparing the genomic features of different organisms, such as DNA sequences, genes, and gene order. This field has revealed both similarities and differences between organisms that can provide insights into evolutionary relationships. Some of the first comparative genomic studies compared large DNA viruses. Since then, many complete genome sequences have been determined, including for yeast, fruit flies, worms, plants, mice, and humans. While humans have around 35,000 genes, complexity is not solely due to gene number. Comparative analysis of human and mouse genomes shows 40% sequence similarity and similar gene numbers, but different genome sizes. Mitochondrial genomes also yield insights when compared between domains of life. Computational tools like BLAST are used to facilitate genomic

1. COMPARATIVE GENOMICS IN EUKARYOTES &ORGANELLES
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By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. contents
 WHAT IS COMPARATIVE GENOMICS?
 HISTORY
 SOME RELATED TERMS
 MINIMAL EUKARYOTIC GENOMES
 COMPARISON OF THE MAJOR SEQUENCED GENOMES
 EUKARYOTIC GENOMES
 SACCHAROMYCES CEREVISIAE GENOME
 INSECT GENOME
 DROSOPHILA MELANOGASTER (FRUIT FLY) GENOME
 COMPARATIVE ANALYSIS OF THE HUMAN AND MOUSE GENOME
 COMPARATIVE GENOMICS OF ORGANELLES
 COMPARATIVE GENOMICS TOOLS
 CONCLUSION
 REFERENCES
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3. WHAT IS COMPARATIVE GENOMICS?
 Comparative genomics is a field of biological research in which the genomic features of
different organisms are compared.
 The genomic features may include the DNA sequence, genes, gene order, regulatory sequences,
and other genomic structural landmarks.
 In this branch of genomics, whole or large parts of genomes resulting from genome projects are
compared to study basic biological similarities and differences as well as evolutionary
relationships between organisms.
 The major principle of comparative genomics is that common features of two organisms will often
be encoded within the DNA that is evolutionarily conserved between them.
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4. HISTORY
 In 1986, the first comparative genomic study at a larger scale was published,
comparing the genomes of varicella-zoster virus and Epstein-Barr virus that contained
more than 100 genes each.
 The first complete genome sequence of a cellular organism, that of Haemophilus
influenzae Rd, was published in 1995.
 The second genome sequencing paper was of the small parasitic
bacterium Mycoplasma genitalium published in the same year.
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5. SOME RELATED TERMS
 Homology: - homology is the relationship of any two characters (such as two proteins that have similar sequences)
that have descended. Usually through divergence, from a common ancestral character.
 Homologues: - homologues are thus components or characters (such as genes/proteins with similar sequences) that
can be attributed to a common ancestor of the two organisms during evolution. Homologues can either be
orthologues, paralogues, or xenologues.
 Orthologues:-orthologues are homologues that have evolved from a common ancestral gene by speciation. They
usually have similar functions.
 Paralogues: - Paralogues are homologues that are related or produced by duplication within a genome. They often
have evolved to perform different functions.
 Xenologues:- xenologues are homologues that are related by an interspecies(horizontal transfer) of the genetic
material for one of the homologues.
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6. Minimal eukaryotic genomes
 A eukaryotic parasite, Encephalitozoon cuiculi, has a genome of only 2.9 Mb and that of a close relative,
Encephalitozoon intestinalis, ~2.3Mb.
 These genomes contain very little repetitive DNA other than rDNA and probably contain less than 2000 genes.
 This is still 7-8 times greater than small prokaryotic genome and it is hard to predict how many of these genes will
be involved in mitotis and related events.
 The change from a prokaryote to a eukaryote does not require a major increase in genome size.
 Of the multicellular organisms whose genomes have been sequenced, Arabidopsis, Caenorhabditis and Drosophila
encode approximately similar numbers of proteins (11000-18000)
 Among vertebrates, Japanese puffer fish(fugu rubripes) has the smallest genome identified to date but has a similar
gene repertoire to other vertebrates such as humans.
 Whereas about 35000 genes are spread over 3000Mb of DNA in human genome these same genes are restricted to
just 400Mb.
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7. Comparison of the major sequenced genomes
 The conservation of a preferred exon size across the three animal genomes suggest a
conserved exon based component of the splicing machinery.
 There are about 35000 genes in the human sequence compared with 6000- yeast,
13000- worm, and 26000 for a plant.
 Humans do not get their complexity over worms and plants by using many more genes
i.e. the number of protein do not account for the physical and behavioural differences
between species.
 Analysis of the genome sequences revealed that over 90% of the domains that can be
identified in human proteins are found in Drosophila and Caenorhabditis protein as
well.
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8.  Enhancer: - they are regulatory element and they are transcriptional activator.
 Cluster of enhancer elements are conserved in mammals.
 Silencers:-they suppress transcription process.
 Sequencing of chicken CD4 gene showed that it is similar to mammalian CD4 gene and has a functional human
silencer.
 It is also present in various type of eukaryotes.
 Insulator elements: - they are the barriers that separate domains within chromatin and confine the actions of
regulator to their target.
 They can block the action of enhancer.
 There is conserved insulator regions that flank beta- globin loci in mouse and man.
 Matrix attachment regions: - MARs are regions of DNA that are involved in the binding of nuclear matrix.
 Several segments are conserved in mouse and man.
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9. EUKARYOTIC GENOMES
 Saccharomyces cerevisiae genome
 One of the most important fungal organisms used in biotechnological processes..
 Considered as a model eukaryotic organism in molecular and cell biology.
 The first eukaryotic organism to have its entire genome sequenced.
 16 chromosomes(2n)
 Approximately genome size- 15520 kb
 5885 potential protein- coding genes.
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10. INSECT GENOME
 Drosophila melanogaster (fruit fly) genome
 It is a species of fly in the family of drosophillidae.
 It is a common pest in homes, restaurants and other occupied places where food is
served.
 Interestingly, the Drosophila Genome contains genes that are similar to 177 of 289
humans genes that are responsible for disease.
 Has been the most important tool for genetics studies in the twentieth century.
 Second multicellular organism to have its genome sequenced.
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12. COMPARATIVE ANALYSIS OF THE HUMANAND MOUSE GENOME
 The mouse genome is 14% smaller than the human genome.
 At the nucleotide level, approximately 40% of the human genome can be aligned to the mouse genome.
 The mammalian genome is evolving in a non-uniform manner.
 The mouse and human genomes seem to contain about 30000 protein-coding genes.
 Similar types of repeat sequences have accumulated in the corresponding genomic regions in both species.
 Genome size:-
 Human :- 2800 Mb
 Mouse :- 2400 Mb
 Rat :- 2500 Mb
 ~1 billion nucleotide are same in all 3.
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14. Comparative genomics of organelles
 Mitochondrial gene:- Animal and fungal mtDNA are much smaller (15-20kb) than plant mtDNA
(200-2000kb).
 Larger size of plant mitochondria is due to more spacer DNA .for example Arabidopsis mtDNA is 20 times
much bigger than human mtDNA but has less than twice the number of gene.
 Mitochondria are considered to be originated from Rickettsia prowazekii the causal agent of typhus
 The structure, organization and gene content of this bacteria is closely resembles that of mtDNA of
Reclimonas Americana.
 2 types of mtDNA :-
 Ancestral mtDNA: - It is similar desidents of bacterial endosymbiont becoz rRNA genes encodes rRNA
gene eubacteria like 235, 165 & 58 ribosomal RNAs & these contains few or no introns.
 Derived mt-DNA:- - it is completely differ from ancestral mt DNA.
 In animals are sub reduction in mt DNA size and in gene contain while in plants particularly in angiosperm
has exsensive gene lose but size has increased by a DNA duplication and capture of sequences from
nucleus and chloroplast.
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16. Comparative genomics tools
 Similarity search programs
 BLAST
 FASTA
 Clustal omega
 MU Mmer (Maximal Unique Match)
 Other alignment programs
 DBA(DNA block aligner)
 Blastz
 BLAST/AVID – WABA(Wobble Aware Bulk Aligner)
 DIALIGN(Diagonal ALIGNment)
 SSAHA(Sequence Search and Alignment by Hashing Algorithm)
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19. conclusion
Comparative genomics has revealed high levels of similarity between closely
related organisms, such as humans and chimpanzees, and, more surprisingly,
similarity between seemingly distantly related organisms, such as humans and
the yeast Saccharomyces cerevisiae.
There are many bioinformatics software used for comparing genomes.
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20. REFERENCES
 https://www.google.co.in/search?q=saccharomyces+cerevisiae+genome&rlz=1C1CHWA_enI
N647IN647&oq=sa&aqs=chrome.1.69i59l2j0j69i57j69i60j69i61.3105j0j7&sourceid=chrome&ie
=UTF-8
 vosshall.rockefeller.edu/reprints/RubinLewisScience00.pdf
 www.nature.com › nature reviews genetics › review
 https://pdfs.semanticscholar.org/23e6/12cac817de60abd4b019131ea335898ab34a.pdf
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21. Thank you
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