Chapter 21 Eukaryotic Genome Sequences

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

Human Sequencing Human Genome Project – 1990-2003 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

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

Techniques Metagenomics – DNA from entire group of species is collected from an environmental sample and sequenced with software - mostly microbial communities - 2012 human microbiome - ability to sequence in mixed populations eliminates need to culture species separately in lab

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

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 1500 more base pairs in DNA compared to bacteria, but only 5 to 15 times more genes

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

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

Movement of Transposable Elements

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

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

Unequal Crossing Over

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