Marine population genetics intro to genetics

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doncheto
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307039
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Marine population genetics intro to genetics
Updated:
2015-09-14 13:28:24
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genetics
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intro vocab
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  1. DNA
    • Deoxyribonucleic acid (DNA)
    • • An alphabet of 4 leFers
    • – adenine (A)
    • – guanine (G)
    • – cytosine (C)
    • – thymine (T)
    • • Sugar backbone
    • – deoxyribose
    • • Direc;onal (has polarity)
    • – 5’ phosphate group
    • – 3’ hydroxyl group
    • Double-stranded
    • – Allows easy replica;on
    • • In base pairs
    • – A-T
    • – C-G
    • – “Reverse-complement”
    • • Packaged into
    • chromosomes
    • – Humans: 23 pairs of
    • chromosomes (46 total)
    • – Fruit flies: 4 pairs (8 total)
  2. Types of DNA
    • nucDNA in the nucleus
    • • Mitochondria have mtDNA
    • • Chloroplasts have cpDNA
  3. central dogma
    • • DNA provides
    • instruc;ons for making
    • RNA
    • • RNA
    • – can act on own OR
    • – template for making
    • proteins (mRNA)
    • • Proteins: the major
    • machinery for cells
  4. Gene structure: coding genes
    • • Promoter: start transcrip;on
    • • Exons: expressed
    • • Introns: intergenic regions
    • • Transcrip;on only occurs from the
    • “coding strand” (other would produce
    • junk)
  5. genes
    • – rela;vely small propor;on of genome (<5% in some cases), but varies among species
    • – ~23,000 genes in humans, ~13,000 in fruit flies
    • – number of genes does not scale with organism complexity
  6. Regulatory regions
    • – contain binding sites for transcrip;on factors
    • – affect rate and occurrence of transcription
  7. Repetive regions
    satellites, minisatellites, microsatellites
  8. Transposable elements:
    • elements that can copy themselves around the genome. SINES and
    • LINES (short and long interspersed nuclear element). Can disrupt or change gene function.
  9. Pseudogenes:
    non-functional copies of coding genes
  10. Ultra-conserved elements
    • – 481 iden;cal regions of at least 200bp found between mouse, human, and rat (Bejerano
    • et al. 2004 Science)
    • – Function unclear
  11. Methylation:
    • attach methyl group to cytosine (5-methylcytosine), usually inactivates a gene.
    • Can be inherited across cell divisions, but low fidelity. A focus of epigenetics.
  12. Ribonucleic acid (RNA)
    • • Usually single-stranded
    • • Sugar backbone has ribose
    • instead of deoxyribose
    • • Four leFers
    • – Adenine
    • – Cytosine
    • – Guanine
    • – Uracil (U): very similar to
    • thymine (T)
    • • Secondary and tertiary
    • structure ohen important
  13. mRNA
    messenger from DNA to protein
  14. tRNA
    • delivers (‘transfers’) amino acids to the translation
    • process
  15. rRNA
    • form structure of the ribosome (along with
    • proteins) for translation
  16. siRNA
    • small, interfering molecules (20-25bp) that reduce
    • expression of specific genes
  17. miRNA
    • micro RNAs (21-23bp) that bind to
    • complementary mRNA strands and prevent transla;on.
    • Less specific than siRNAs.
  18. introns
    • – spliced out of mRNA
    • – alterna;ve splicing
    • possible and important
  19. Exons
    • – Untranslated Region
    • (UTR): stability,
    • localiza;on, efficiency
    • – Coding sequence (CDS) for
    • protein sequence
  20. genetic code
    • • Translates nucleotide triplets into
    • amino acids
    • • Code varies somewhat between
    • nucDNA vs. mtDNA
    • • Start (AUG/ATG) and stop codons
    • for transla;on
    • • Redundant codes for the same
    • amino acid
    • – Synonymous muta;ons: change
    • the nucleo;de but not the amino
    • acid (ohen 3rd position)
    • • fourfold degenerate (e.g., Val)
    • • twofold degenerate (e.g., Tyr)
    • – Non-synonymous mutations
  21. locus
    • a segment of the genome, used to
    • refer to a gene or other genetic marker
  22. allele
    • alternative forms of the same locus
    • (i.e., a difference in sequence, maternalpaternal)
  23. Allozymes
    • • Different forms of the same protein
    • – detects amino acid differences (coarse)
    • – distinguish by size and/or electric charge
    • • Run on an electrophoresis gel
    • • Different forms of the same protein
    • – detects amino acid differences (coarse)
    • – dis;nguish by size and/or electric charge
    • • Run on an electrophoresis gel
    • – Produces distinctive bands at specific places
  24. allozyme limitations
    can't spot silent mutation
  25. mtDNA/cpDNA sequencing
    • Read sequence directly: AAGT, etc.
    • • Maternally inherited (except molluscs
    • and rare excep;ons)
    • • Cytochrome oxidase I (COI): common
    • for iden;fying species
    • • Control region: higher subs;tu;on
    • rate, greater diversity (doesn’t code
    • for proteins)
    • • Cytochome b (cyt b): intermediate
    • muta;on rate
    • • Only a single locus (n = 1)
  26. Restriction fragment length
    polymorphisms (RFLP)
    • • Assays DNA directly
    • • Restriction enzymes found naturally in
    • bacteria
    • • Bind to a specific DNA sequence
    • – Won’t bind if there has been a
    • mutation at the cut site
    • • Cut the strand
    • – Leaves a blunt or a sticky end
    • • Run product on a gel, assess variation
    • in length
    • • Ohen used with mtDNA
    • – Most popular in 80s and 90s
    • – Cheap
  27. nucDNA
    • Poten;al for many loci: greater
    • power for inference
    • • Can examine protein-coding loci
    • • Exons or introns
    • – Exon-priming, intron-crossing (EPIC)
    • primers: more likely to work across
    • species
  28. Microsatellites
    • • Repetitive sections of the genome
    • – AT AT AT AT AT
    • – GTA GTA GTA GTA
    • – 2-5 bp repeats
    • • Strands can slip during replica;on or recombination
    • – adds or deletes a repeat
    • – changes length of microsatellite locus
    • – Frequent muta;on: loci are highly polymorphic
    • • Assess variation in fragment length on a gel
  29. Single Nucleotide Polymorphism (SNPs)
    • • Usually from nucDNA
    • • A single position in the genome that can be one of
    • two alternate bases
    • • Need primers (flanking sequence)
    • – ohen developed from genome
    • • Only see the SNPs that you look for (ascertainment
    • bias)
  30. Transcriptomes
    • • All mRNA in a tissue
    • • Transcribed genes ~5% of genome
    • • Genes likely to be functional
    • • Can identify sequence AND level of expression
    • (# transcripts)
  31. Genotyping by sequencing
    • • Various methods to select a repeatable
    • subset of the genome
    • – e.g., cut with restric;on enzymes and sequence
    • near cut-sites (RADseq, RRL, CroPS)
    • • Efficient use of next-gen sequencing for
    • popula;on-level or phylogene;c ques;ons
    • – e.g., 300 thousand bp from each of 10,000
    • individuals instead of 3 billion bp from 1
    • individual
  32. Sanger sequencing
    • • Developed by Frederick Sanger and
    • colleagues in 1977
    • • Outline is similar to PCR: polymerase copies
    • a DNA strand
    • • Copying starts from primers
    • – can be same as used in PCR
    • • Uses a mix of normal (dNTP) and dideoxy
    • nucleotides (ddNTP)
    • – H instead of OH at 3’ and 2’ posi;on on sugar
    • backbone
    • – cannot be extended further by polymerase
    • • ddNTPs are fluorescently labelled
    • – 4 colors for 4 nucleotides
    • • Creates DNA copies that terminate at
    • random positions
    • – Hence, called the “dye-termination” method
    • – Generates forward and reverse strands that
    • may overlap in the middle
    • • Run fragments through a gel,
    • separate by size
    • – Capillary gel on an automated
    • sequencer
    • • Read sequence of fluorescing
    • dyes with a laser
    • • Fragments up to 1000 bp
    • – $2-3/sequence (250bp/$)
    • • Widely available as a
    • commercial service
  33. Illumina sequencing (aka Solexa)
    • • Most popular of next-gen technologies
    • • Reads 33-300 bp at either end of a DNA
    • fragment
    • • Up to 280 million reads per run
    • – $1k -4k per run (12 million bp/$)
    • – Available from sequencing centers (e.g.,
    • Princeton LSI, UC Berkeley)
    • • Can put mul;ple samples on a lane, iden;fy
    • later by DNA “barcode”
    • • Process:
    • – AFach DNA fragments to surface of a glass slide
    • (“flow cell”)
    • – Amplify into a cluster
    • – AFach a fluorescently labeled dNTP
    • – Image
    • – Remove fluorescent label
    • – Add next fluorescently labeled dNTP

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