1. Chapter 21 Eukaryotic Genome Sequences

2. Genomics
Genomics and the ability of sequencing entire genomes has generated and continues to generate volumes of data
Bioinformatics – application of computational methods to store and analyze biological data

3. Human Sequencing
Human Genome Project – completed when the nucleotide sequence of majority of DNA in each human chromosome was obtained.
-researchers have also mapped sequences for E coli, yeast, corn, nematodes, fruit flies, orangutan, and the house mouse
- since 2006 project deemed virtually complete with each nucleotide sequence from each chromosome
- helped develop the technology for sequencing and increased rate from 1,000 base pairs a day to 1,000 pairs per second
2. Physical mapping
3. DNA sequencing

4. Techniques
Whole genome shotgun approach – cloning and sequencing fragments of DNA randomly cut.
Computer programs assemble large overlapping sequences into a single continuous segment

5. Techniques
Metagenomics – DNA from entire group of species is collected from an environmental sample and sequenced with software
- mostly microbial communities
human microbiome
- ability to sequence in mixed populations eliminates need to culture species separately in lab

6. Protein Coding Genes
Gene annotation – process to identify all protein coding genes in a sequence and their functions
- automated software that scans sequence for transcriptional or translational start and stop signals
- also scan for mRNA’s (ESTs –expressed sequence tags – identifying unknowns

7. Size, Genes, & Density Eukaryotes have larger genomes than bacteria
Plants contain the largest sets of genes
Gene density tells a different story because of noncoding DNA
Coding for proteins and RNA products is only a tiny portion of the genome
Bulk of genomes is mostly noncoding or “junk DNA”
*Must have important role to persist for hundreds of generations
Ex: human genome has 500 to more base pairs in DNA compared to bacteria, but only 5 to 15 times more genes

8. Human Genome Sequences
Regulatory sequences and introns account for vast differences in eukaryotic genome vs. prokaryotes
Pseudogenes – gene fragments that contain mutations and no longer code functional proteins
Repetitive DNA which is DNA present in multiple copies, represents the largest portion in the genome, specifically if it includes transposable elements

9. Transposable Elements
Transposable elements represents DNA that can move to other locations within the genome.
2 types:
1. Transposons - use cut and paste or copy and paste method to move in genome by means of a DNA intermediate
Ex: Alu elements – transcribed into RNA
2. Retrotransposons – use copy and paste method with a RNA intermediate, but will use reverse transcriptase to convert back to DNA before reinsertion into genome
*comprises most of transposable elements in eukaryotic genome
Ex: LINE -1 or L1 – may account for differing nerve cell types

10. Movement of Transposable Elements

11. Other Repetitive DNA Nontransposable repeats comprise 15% of genome
-exists as large segment DNA or
-simple sequence DNA consists of many copies of tandem repeats of 5 to 500 nucleotides
*found at telomeres and centromeres and may play a structural role in chromosomes

12. 19.5 Genomic Evolution Factors
Duplication, rearrangement, and mutations are the mechanisms of evolution
- duplications can arise from multiple sets chromosomes – polyploidy
- not as common in animals, but could account 80% of changes in plants today
-extra sets accumulate mutations and usually limit life cycle or if it survives will alter phenotype

13. Unequal Crossing Over

14. Factors of Genome Evolution
Errors in meiosis from unequal crossing over can lead to deletion or duplication of certain region in genome
Slippage of replicated DNA shifts complementary sequences and can lead to errors that delete or duplicate genes
Transposable elements promote recombination of genes, disrupt cellular genes, or carry whole genes and exons to different locations in genome