Key Concepts Once a genome has been completely sequenced researchers use a variety of techniques to identify which sequences code for products and which act as regulatory sites Bacterial and archaeal genomes are relatively small Among species there is a positive correlation between total gene number and metabolic capabilities Gene transfer between species is also common 2011 Pearson Education Inc Key Concepts Eukaryotic genomes are large and complex They include many sequences that have little to no effect on the fitness of the organism and many transcribed sequences whose function is not known Data and techniques derived from genome sequencing projects are being used to analyze cancer cells 2011 Pearson Education Inc Introduction The complete DNA sequence of an organism is its genome The human genome sequence was published in February 2001 as part of the Human Genome Project Genomics is the scientific effort to sequence interpret and compare whole genomes Genomics provides a list of the genes present in an organism Functional genomics looks at when those genes are expressed and how their products interact 2011 Pearson Education Inc Whole Genome Sequencing Improved automation has increased the speed and reduced the cost of DNA sequencing The primary international repositories for DNA sequence data now contain over 194 billion nucleotides With about 3 billion nucleotides humans have the largest haploid genome sequenced to date The size of the database increases by about 30 percent every year 2011 Pearson Education Inc 2011 Pearson Education Inc How Are Complete Genomes Sequenced Bioinformatics is the effort to manage analyze and interpret biological information and is key to managing the vast quantity of data generated by genome sequencing 2011 Pearson Education Inc Which Genomes Are Being Sequenced and Why The first genome of an organism to be sequenced was that of the bacterium Haemophilus influenzae in 1995 it consists of about 1 8 million base pairs The first eukaryotic genome to be sequenced was that of the yeast Saccharomyces cerevisiae in 1996 To date complete genomes have been sequenced from over 800 species Most of the organisms that have been sequenced cause disease or have other interesting biological properties 2011 Pearson Education Inc Which Sequences Are Genes The most basic task in annotating or interpreting a genome is to identify which bases constitute genes Identifying genes is relatively straightforward in bacteria and archaea but is much more difficult in eukaryotes who have many noncoding sequences in their genomes 2011 Pearson Education Inc Identifying Genes in Bacterial and Archaeal Genomes Computer programs are used to scan a genome sequence in both directions in order to identify open reading frames ORFs ORFs are possible genes long stretches of sequence that lack a stop codon but are flanked by a start codon and a stop codon The computer programs also look for sequences typical of promoters operators and other regulatory sites Researchers can confirm that an ORF is actually a gene by analyzing its product or by finding that it is homologous similar due to common ancestry to a known gene 2011 Pearson Education Inc 2011 Pearson Education Inc Identifying Genes in Eukaryotic Genomes In eukaryotic organisms genes contain introns and most of the genome does not code for a product thus it is not possible to scan for ORFs The most effective strategy for identifying genes is to use reverse transcriptase to produce a cDNA version of each mRNA and sequence a portion of the resulting molecule to produce an expressed sequence tag or EST ESTs represent protein coding genes 2011 Pearson Education Inc Bacterial and Archaeal Genomes By sequencing the genomes of various strains of the same prokaryotic species researchers can now compare the genomes of closely related organisms that have different ways of life 2011 Pearson Education Inc The Natural History of Prokaryotic Genomes In bacteria there is a general correlation between the size of the genome and the metabolic capabilities of the organism The function of many bacterial genes is still unknown There is tremendous genetic diversity among bacteria and archaea About 15 percent of the genes in a prokaryotic genome are unique to its own species Redundancy among genes is common Some genes are found multiple times within a prokaryotic genome 2011 Pearson Education Inc The Natural History of Prokaryotic Genomes Multiple chromosomes and plasmids are more common than expected In many bacterial and archaeal species a significant portion of the genome appears to have been acquired from other often distantly related species 2011 Pearson Education Inc 2011 Pearson Education Inc Lateral Gene Transfer The movement of DNA from one species to another species is called lateral gene transfer Recent evidence suggests that over 50 percent of archaean species and 30 50 of bacterial species have at least one gene acquired by lateral gene transfer 2011 Pearson Education Inc Eukaryotic Genomes Many eukaryotic genomes are dominated by repeated DNA sequences that occur between genes or inside introns and do not code for products used by the organism Sequencing eukaryotic genomes presents unique challenges Eukaryotic genomes are much larger than the genomes of bacteria and archaea The presence of noncoding repetitive sequences 2011 Pearson Education Inc Parasitic and Repeated Sequences Protein coding sequences constitute a very small percentage of the human genome and repetitive sequences make up more than 50 percent In contrast over 90 percent of the prokaryotic genome consists of genes Repeated sequences in the human genome are often the result of transposable elements segments of DNA that can move from one location in a genome to another 2011 Pearson Education Inc Characteristics of Transposable Elements Transposable elements are examples of selfish genes parasitic DNA sequences that survive and reproduce but that do not increase the fitness of the host genome Transposable elements are classified as parasitic because they decrease their host s fitness It takes time and resources to copy them along with the rest of the genome They can disrupt gene function when they insert in a new location 2011 Pearson Education Inc Repeated Sequences Eukaryotic genomes have several thousand loci called short tandem repeats STRs These are small sequences repeated down the length of a chromosome There are two types of STRs 1 Microsatellites or simple