Genomics

Lecture 8By Ms. Shumaila Azam

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Genome Evolution

“Genomes are more than instruction books for building and maintaining an organism; they also record the history of life.”

Genome Evolution

• Genome evolution is the process by which a genome changes in structure (sequence) or size over time.

• Key challenge of molecular evolutionary biology is finding a way to use changes in DNA sequences to test ideas of evolutionary biology based largely on morphological characters.

• Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes

History

• The first sequenced genomes became available in the late 1970s

• Scientists have been using comparative genomics to study the differences and similarities between various genomes.

• Genome sequencing has progressed over time to include more and more complex genomes– human genome in 2001

Genome Evolution in Prokaryotes

• Cellular and genomic organization of prokaryotes is different from that of eukaryotes 1. Prokaryotes have no nucleus. 2. The nucleoid region in a prokaryotic cell consists of a concentrated mass of DNA. This mass of DNA is usually one thousand times less than what is found in a eukaryote. 3. A prokaryote may have a plasmid in addition to its major chromosome. A plasmid is a small ring of DNA that carries accessory genes.

•Usually these genes are for antibiotic resistance!•Photosynthesis evolved early in prokaryotic life 1. Cyanobacteria started to produce O2 about 2.7 billion years ago

Mechanism of Evolution in Prokaryotes

• Two methods– mutation and – horizontal gene transfer

Ways to Transfer Genes

• Three (3) ways for genes to be transferred between cells:

• a.  Transformation – cell takes up genes from the surrounding environment.

• b.  Conjugation – direct transfer of genes from one prokaryote to another. Use the pilus to conjugate.

• c.  Transduction – viruses transfer genes between prokaryotes.

Evolution In Eukaryotes

• Eukaryotic genomes are generally larger than that of the prokaryotes.

• The Human genome is much larger with a size of approximately 3.2Gb

• The eukaryotic genome is linear and can be composed of multiple chromosomes, packaged in the nucleus of the cell.

• The non-coding portions of the gene, known as introns• Eukaryotic genomes evolve over time through many

mechanisms including sexual reproduction which introduces much greater genetic diversity to the offspring than the prokaryotic process of replication in which the offspring are theoretically genetic clones of the parental cell.

Multiple Fields

• Structural analysis of the genome• Comparative genomics• Genome duplications

Structural analysis of the genome

• Complete genome sequences exist for a human, chimpanzee, E. coli, brewer’s yeast, corn, fruit fly, house mouse, and other organisms

• Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups

Structural analysis of the genome

• Genomics is the study of whole sets of genes and their interactions

• Bioinformatics is the application of computational methods to the storage and analysis of biological data

Exons (1.5%) Introns (5%)

Regulatorysequences(20%)

UniquenoncodingDNA (15%)

RepetitiveDNA unrelated totransposableelements(14%)

Large-segmentduplications (56%)

Simple sequenceDNA (3%)

Alu elements(10%)

L1sequences(17%)

RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)

Comparative genomics

• Comparative genomics: Comparing genomes (entire DNA sequences) of different species provides a powerful new tool for exploring the evolutionary divergence among organisms

• Genomes are instructions and a history of life• an attempt to take advantage of the information provided

by the signatures of selection to understand the function and evolutionary processes that act on genomes.

• Gene finding is an important application of comparative genomics

Comparative genomics

• Those elements that are responsible for similarities between different species should be conserved through time.

• Those elements responsible for differences among species should be divergent

• Those elements that are unimportant to the evolutionary success of the organism will be unconserved.

Genome Duplication

• Gene duplication is the process by which a region of DNA coding for a gene is duplicated.– Recombination– Retrotransposition event

• Duplicate genes are often immune to the selective pressure under which genes normally exist

• This can result in a large number of mutations accumulating in the duplicate gene code

• the gene non-functional or in some cases confer some benefit to the organism

Whole-genome duplication

• Polyploidy can result from – Three or more chromosome sets– Genome duplication in one species

• Autopolyploids – meiotic error (same species)

– Hybridization of two different species• Allopolyploids – hybridization and duplication of the

genomes of two different species (different species)

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Polyploidy in plants• Occurred numerous times in flowering plants• At least one-half of all plants have evidence of polypoidy.

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