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DNA variation in Ecology and Evolution I- Organization of the genome. Maria Eugenia D’Amato. BCB 703: Scientific Methodology. Aim of the course. Understanding the underlying principles and forces that mold genetic variation in organisms. DNA. Organization of the genetic information.
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DNA variation in Ecology and EvolutionI- Organization of the genome Maria Eugenia D’Amato BCB 703: Scientific Methodology
Aim of the course Understanding the underlying principles and forces that mold genetic variation in organisms • DNA. Organization of the genetic information. • Methodological approaches to the study of genetic variation. Application of molecular markers. • Patterns of genetic variation and inference of underlying processes in natural populations
Domestication: an early understanding of transmission of characters. Early Neolithic wild Bronze Age Present day Ovis orientalis Maize
Discovery of the mechanisms of inheritance Cross-pollination experiments with peas Gregor Mendel (1822- 1884)
Mendelian laws of inheritance Parental genotype GgWw Parental genotype GgWw • Independent assortment • Independent segregation • Dominant-recessive
Meiosis 4c 2c 2c 2c c Homologous chromosomes segregate 2 haploid cells with duplicated genetic material Sister chromatides segregate 4 haploid cells
Mitosis 2N - Homologous chromosomes 2C Homologous chromosomes duplicate information 4C Sister chromatides separate 2N chromosomes 2C
Organization of the genetic information Animal cell Plant cell
Nuclear genetic information Condensation of chromatin Human karyotype
Molecular structure of DNA 5’ Purines 3’ Pyrimidines H-bond 3’ 5’
Discovery of DNA molecular structure James Watson Francis Crick (1928- ) 1916-2004 Nobel Price 1962 Rosalind Franklin 1920-1958 Maurice Wilkins 1916-2004 Nobel Price 1962
Nuclear DNA: coding and non-coding sequences • Coding DNA Genes. • Ribosomal and transfer RNA. Satellite DNA Introns Microsatellites Transposon-like elements • Non-coding DNA Regulatory regions Interspersed repetitive DNA
Genes: the coding DNA The role of the three types of gene products: mRNA, tRNA, rRNA tRNA Yeast 18S and 5.8 S rRNA
Genes: organization of rRNA and tRNA tRNA and rRNA genes are organized in clusters of repeats rDNA repeat unit Ribosomal genes Nucleolus-organizing region in wheat
Gene families: concepts Orthologs Homologs Paralogs Identity by descent different function time Identity by descent Similar function Identity by descent
Non-coding DNA1. Satellite DNA ATTCATTCGATATAAAAAAACGTATATTA…. • Repeats = 100s -1000s • base pairs • centromeric- telomeric position
Non-coding DNA2.Minisatellites and the origin of DNA fingerprinting Locus 1 (GATTTAA)9 (GATTTAA)7 • VNTR, 10-100 bp repeats • Mostly subtelomeric position • Individual identification Sir Alec Jeffreys
Non-coding DNA3. Microsatellites • (AC)n, (ACT)n, (AGTA)n, etc • STR, simple sequence repeats stretches of 2-6 bp • Allelic number is high, mutation rate high. • Accurate individual identification. • Use in genome mapping, forensics, population studies, • pedigree reconstruction, etc.
Mobile elements.The origin ofinterspersed repetitive DNA • Fragments of DNA that self-propagate within cell genome • Cause mutations • Challenge the central dogma • of molecular biology Barbara McClintock, 1902-1992. Nobel Price 1983
Mobile elements: Retrotransposons LTRs • RNA is copied into DNA and inserted elsewhere in the genome • 40% of human genome is composed of retroelements • Propagation similar to retroviral infections (HIV, HTLV, etc) • LINES • SINES (Alu elements) RNA cDNA Target DNA insertion
The other genome:mitochondrial DNA • Coding for 13 proteins, 22 tRNA, 2rRNA • Maternally inherited • Higher evolutionary rate than nuclear DNA • Utilized in the study of • microevolutionary processes, phylogenetics, • phylogeography, etc
The genetic code • Information coding for aminoacids is carried by codons in DNA and recognized by the anticodons in the tRNA • The genetic code is redundant • Different code for mtDNA, nuclear DNA, clDNA and taxonomic levels.
Genetic code: examples Hystidine. Transversion in 3rd position changes to Glutamine 2-fold degeneracy Alanine 4-fold degeneracy Serine is coded by 6 different codons Krill COI Glycine changes to Cysteine Change in 1st position 0-fold degeneracy Q
Change in the heritable material Raw material of evolution Source of variation to be affected by evolutionary processes The origin of genetic variation: MUTATIONS Point mutations Gene duplication Chromosomal rearrangements Polyploidization Types
Types of mutations • Single point • Insertions • Deletions Synonymous Protein coding genes Non-synonymous Intronic regions Number of repeats in microsatellites Within loci Changes in RNA genes
Point mutations Transversions A T Purine- Purine Transitions C G Pyrimidine- Pyrimidine
Insertions and deletions • Reading frame changes in protein-coding regions. Asn Arg Leu Ser Arg AAT CGA TTA TCT AGG AAT ACG ATT ATC TAG G.. Single point insertion Asn Thr Ile Ile STOP New reading frame
Insertions and deletions Krill ITS-1 CCCCCATCA CCCCC-TCA
Chromosomal rearrangements + A B C D E F A B E D C F A B C D E F A B C D G H I D G H I J K J K E F Inversion Fusion Translocation
Ploidy: number of single sets of chromosomes in a cell or organism Changes at the ploidy level • Polyploidy is a common speciation processes in plants • Tetraploids: maize, cotton, leek • Hexaploids: wheat, oat. • Octaploids: strawberries, sugar cane.
How often do mutations occur? Mutation rate : the number of mutation events per gene per unit of time Mutation rates per generation Per base pair ~10-8 - 10-9 nuclear coding Per gene ~10-6 - 10-5 Per genome ~0.02 - 1 Microsatellites per loci 10-3 - 10-4 HVR human mtDNA 4.3 10-3
Molecular clocks A C B • Constant mutation rate • Inference of divergence time time