TAILIEUCHUNG - Lecture AP Biology - Chapter 21: Genomes and their evolution

This chapter explain how linkage mapping, physical mapping, and DNA sequencing each contributed to the Human Genome Project, define the fields of proteomics and genomics, describe the surprising findings of the Human Genome Project with respect to the size of the human genome, distinguish between transposons and retrotransposons. | Genomes and Their Evolution What you need to know: The major goals of the Human Genome Project How prokaryotic genomes compare to eukaryotic genomes. The activity and role of transposable elements and retrotransposons. How evo-devo relates to our understanding of the evolution of genomes. The role of homeotic genes and homeoboxes. Bioinformatics Use of computers, software, and math models to process and integrate data from sequencing projects Human Genome Project Purpose: to sequence the entire human genome Completed in 2003 Genomes sequenced thus far*: 58,000 prokaryotes, 2700 eukaryotes, 5300 viruses * Data as of 1/27/16 Human DNA 3 billion base pairs ~20,000 genes Only codes for proteins (or RNA) Mostly Repetitive DNA: sequences present in multiple copies Transposable Elements Make up 75% of repetitive DNA Stretches of DNA that can be moved from one location to another in genome Discovered by Barbara McClintock – corn breeding experiments 2 Types: Transposons Retrotransposons Transposons Moves within genome via DNA intermediate “cut & paste” or “copy & paste” mechanisms Requires enzyme transposase Retrotransposons Move by means of RNA intermediate Leaves copy at original site Involves enzyme reverse transcriptase Genome Evolution Insertion effects of transposons: Can interrupt or alter gene function Multiple copies of genes Duplication genes with related functions Genes diverge by accumulating mutations Some become nonfunctional pseudogenes Eventually, new genes with new functions can occur Multigene Families Collections of 2 or more identical or very similar genes Eg. hemoglobin: -globin and -globin gene families Transposable elements contribute to evolution Promote recombination, disrupt genes or control elements, & carry genes to new locations May be harmful or lethal, but can also have small beneficial effects Provides raw material for natural selection Illustrative Example: Antifreeze Gene in Fish Antifreeze proteins (AFP): produced by vertebrates,

• Sinh học
• Genome sequencing
• Gene density
• Lecture AP Biology
• Systems biology
• Biological sciences
• Biological organization
• Genome Biology
• Third generation sequencing platform
• Single molecule sequencing
• Single cell genome sequencing
• Structure variants
• Extra chromosomal circular DNAs
• Pan genome
• Accessory genome
• Whole genome sequencing
• Next generation sequencing
• Genome wide association studies
• BMC Bioinformatics
• Genome coverage
• Sequencing depth
• Multisample calling algorithms
• BMC Genomics
• Borrelia miyamotoi
• Reference genome
• Long read sequencing
• Lyme borreliosis
• Human embryonic stem cell
• Genome editing
• Nanopore sequencing
• Somatic mutation
• Structural variant
• High coverage whole genome sequencing
• Variant analysis
• Vietnamese human genome
• Illumina sequencing machines
• Mapping precision
• False positive rate
• Genome wide polymorphisms
• Genome differentiation
• RNA sequencing
• Diploid species
• Genetic map
• K mer
• Genotypeby sequencing
• Genome assembly
• Chromosome scale genome assembly
• Protein coding genes
• Exome sequencing
• BMC Veterinary Research
• Tiling PCR
• Amplicon sequencing
• Single molecule real time sequencing
• Linked read sequencing
• Optical mapping
• Bacterial genomics
• Oxford Nanopore sequencing
• Structural variation
• Copy number variation
• Human diseases
• Genome assembly and scaffolding
• High throughput sequencing
• Pooled clone sequencing
• Organismal evolution
• BMC Cancer
• HPV integration
• High risk human papillomaviruses
• Precision oncology
• Whole genome amplification
• Single cell sequencing
• Multiple displacement amplification
• Variant calling
• Human genomes
• Mycobacterium tuberculosis
• Drug resistant tuberculosis
• Within patient diversity
• HLA genotyping
• Whole exome sequencing
• Cancer immunogenomics
• Bayesian hierarchical model
• Markov chain Monte Carlo
• Web tool
• Bacterial genome
• Genome finishing
• Genome sizing
• Genome analysis
• Whole genome
• Nextgeneration sequencing
• DNA sequence
• Compact genome
• Genome architecture
• Extreme environment fungi
• Genome compaction
• Batch effects
• Principal components analysis
• Genome scaffolding
• Marine Synechococcus