689 Special Topics in Ecological Genomics. Spring January 20, 2015

Transcription

1 689 Special Topics in Ecological Genomics Spring 2015 January 20, 2015

2 Dr. Claudio Casola, Assistant Professor in Forest Genomics, Department of Ecosystem Science and Management Phone: (979) Office hours: Monday or by appointment Office: HFSB 317

3 Course Topics, Calendar of AcJviJes, Major Assignment Dates Readings and discussions: Except for the computer demonstranons, each session will consist in the discussion of an assigned book chapter or papers. Papers discussion will be led by students, with exact dates to be determined at the beginning of the semester. When leading the discussion, students will prepare a PowerPoint presentanon with informanon about the background, methodological approach and main findings of the arncle, including tables/ figures in the main text and supplementary online material or other material if deemed interesnng. The presennng student is encouraged to prompt the discussion with quesnons to the audience. MeeNng with the instructor a week or a few days before presennng the paper is recommended. Online resources to help put together an effecnve presentanon and leading a discussion will also be provided. Requirement: 3 presentajons per student

4 Resources to present a paper UC Davies Graduate Studies h\p://gradstudies.ucdavis.edu/professional- development/gradpathways/ presentanon- skills Towson University- Guidelines For Student PresentaNons In Class h\p://grad.towson.edu/program/master/hurd- hrdg- ms/files/guidelines %20For%20Student%20PresentaNons%20In%20Class.pdf UNC poster and presentanon resources (lots of links) h\p://gradschool.unc.edu/academics/resources/posternps.html#prez

5 Course Topics, Calendar of AcJviJes, Major Assignment Dates Homework: Wri\en homework will be assigned in class and/or on the course website, usually about once a month. The objecnve of the homework is to help students pracnce the nuts- and- bolts computanons of populanon genencs, populanon genomics and transcriptomics, using available data sets. Answers to the homework will be available on the course website within 1-2 days aeer the class session at which the homework is due. Late assignment submissions will not be accepted, unless prearranged with the instructor or in an emergency situanon.

6 Course Topics, Calendar of AcJviJes, Major Assignment Dates WriTen Paper and final presentajon: Students will write a literature review of a topic of choice in ecological genomics. The subject of the review will be discussed with the instructor no later then March 12 th. This assignment will be graded on the basis of the quality of the points presented, the skill with which the arguments are made, as well as the quality of the wrinng. [ ] The main points of the review will be presented by each student in a 15 minutes talk toward the end of the course. This assignment can also be a project by a single person or a group

7 Grading Overall course percentage grade will be determined from a weighted average of: ParNcipaNon in discussions (20%) Leading discussions (20%) 4 homework (30% total) Wri\en paper and final presentanon (30%)

8 QuesJons about the reading assignments?

9 A Timeline of Genomics NHGRI National Human Genome Research Institute h\p://

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12 The human genome project(s) February 2001

13 First sequenced genomes: viruses 1976, Fiers et al.: bacteriophage MS2, first sequenced genome, RNA genome (3,569 base pairs, Accession NC_001417). 1977, Sanger et al.: bacteriophage φx174 genome, DNA genome. 11 genes. (5,386 base pairs Accession J02482; NC_001422) David T. Denhardt 0.5 µm h"p://users.rcn.com/jkimball.ma.ultranet/ BiologyPages/PPhiX.html

14 Genomes and Databases Sequence Accession numbers are IDs that allow sequences to be easily deposited in and retrieved from online databases DDBJ, EMBL, GenBank The three main sequence databases. They are redundant and work in concert GenBank is the NIH genenc sequence database, an annotated collecnon of all publicly available DNA sequences GenBank is maintained by the NCBI (NaNonal Center for Biotechnology InformaNon)

15 The Structure of DNA

16 April, 1953

17 NucleoNdes

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19 The double helix DNA normally consists of two annparallel polynucleonde chains sugar phosphate backbone phosphodiester bonds 5 to 3 connecnon complementary base pairs A T G C hydrogen bonds 2 per A T 3 per G C 5 3 chain polarity Major and minor grooves (see model) AATTGGCCGATC-3 3 -TTAACCGGCTAG-5

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21 DNA features ReplicaNon: each strand serves as template for synthesis of complement, using rules of base pairing InformaNon: specified by sequence of nucleondes; may be copied into RNA MutaNon: replacement, insernon, delenon of nucleonde results in altered sequence

22 The Structure of Genes

23 Gene: definijons Molecular Cell Biology. 4th edijon (2000) h\p:// In molecular terms, a gene commonly is defined as the en@re nucleic acid sequence that is necessary for the synthesis of a func@onal polypep@de. [AND ALSO MANY TYPES OF RNAs WITH STRUCTURAL OR REGULATORY FUNCTIONS] What is a gene, post- ENCODE? History and updated definijon (2007) h\p://genome.cshlp.org/content/17/6/669.full A gene is a union of genomic sequences encoding a coherent set of potennally overlapping funcnonal products. The term "gene" is shared by many disciplines, including classical genetics, molecular genetics, evolutionary biology and population genetics. Because each discipline models the biology of life differently, the usage of the word gene varies between disciplines. It may refer to either material or conceptual entities.

24 Structure of genes Gene = transcripnonal unit Gene encodes coding RNA (mrna) or non- coding RNA (trna, rrna,mirna...) regulatory region DNA encoding funcnonal RNA RNA primary transcript Gene is a funcnonal element of the chromosome and is transcribed into RNA at the correct Nme and place in development or cell cycle To some researchers, gene actually includes its adjacent regulatory region(s)

25 EukaryoNc genes: introns and exons Intron: noncoding region of gene, excised by processing from primary transcript (=splicing) zero to many per eukaryonc gene variable length, may account for most of gene length FuncNon of introns poorly understood (no generic funcnon known, but they oeen contain regulatory sequences) Exon: coding region of gene (exon sequence is included in mature transcript) transcript E1 I1 E2 I2 E3 I3 E4 nuclear processing steps mature transcript E1 E2 E3 E4

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27 The Structure of Genomes

28 What is a genome? The genome represents the whole hereditary informanon of an organism It is physically formed by DNA, except in some viruses where it is consntuted by RNA

29 The nature of genomes Prokaryotes One circular chromosome Zero- many plasmids Eukaryotes One nuclear genome, usually several chromosomes mitochondrial genomes chloroplast genomes in plants/algae

30 ProkaryoNc genome Usually circular double helix Gene- dense: genes are close together with li\le intergenic spacer Genes are oeen organized in operon tandem cluster of coordinately regulated genes Several genes transcribed as single mrna No spliceosomal introns

31 Prokaryotes: one genome per cell plus plasmids

32 Circle representanon of the genome of E. coli K- 12

33 Figure 1 The overall structure of thee. coli genome. F R Blattner et al. Science 1997;277: Published by AAAS

34 Eukaryotes: 2 or 3 different genomes per cell

35 The Mitochondrial Genome A map of the human mitochondrial genome - Circular, 2-10 copies per mitochondrion - Resembles a reduced prokaryonc genome in terms of organizanon and gene numbers - The human mitochondrion genome encodes 37 genes: 13 protein- coding genes involved in the producnon of energy (oxydanve phosphorylanon) and 24 non- coding genes involved in mrna translanon (trnas, rrna) - Maternally inherited

36 Mitochondrial genomes can vary in size between species Human (mammal) 16.5 kb MarchanJa (moss) 186 kb Yeast (fungus) 75 kb

37 The Chloroplast Genome (plants) MarchanJa (moss) CpDNA 121 kb - Circular - Resembles a reduced prokaryonc genome in terms of organizanon and gene numbers - Encodes genes mostly involved in photosynthesis and electron transport - Maternally inherited (transmi\ed through the seed) - Do not vary much in size

38 mitochondrion chloroplast Lack mitochondria (?)

39 Databases: NCBI Organelle genomes (NaNonal Center for Biotechnology InformaNon) htp://

40 Eukaryotes: 2 or 3 different genomes per cell

41 EukaryoNc nuclear genome: chromosomes Linear structure Chromosome number is conserved within species but greatly varies between species Ploidy refers to number of complete sets of chromosomes haploid (1n): one complete set of genes (e.g. yeast) diploid (2n) (e.g. most animals) polyploid ( 3n) (e.g. many plants, a few animals) In diploids, chromosomes come in homologous pairs (homologs) structurally similar same sequence of genes may contain different alleles

42 Structure of eukaryonc chromosomes Telomere Telomere

43 Chromosome # in eukaryotes Adders- tongue Ophioglossum re@culatum 1200 or 1260 Highest known chr # Jack jumper ant Myrmecia pilosula 2 2 for females, 1 for males (haploid) Fruit fly Drosophila melanogaster 8 6 autosomal, and 2 sexual Baker yeast Saccharomyces cerevisiae 32 THE NUMBER OF CHROMOSOMES DOES NOT CORRELATE WITH THE NUMBER OF GENES!! # of genes: human ~22,000 chicken ~18,000 fruit fly ~14,000 baker yeast ~6,000

44 Very different genome landscapes in prokaryotes and eukaryotes In prokaryotes, genes are compactly arranged, with li\le or no spacer sequences in between (short intergenic regions) = most of the genome is coding DNA In eukaryotes, there is considerable spacer DNA between genes (large intergenic regions) and within genes (introns) = most of the genome is non- coding DNA

45 Genome Size Units of measurement base pair (bp) kilobase (kb) = 1,000 bp megabase (Mb) = 1,000,000 bp Gigabase (Gb) = 1,000,000,000 bp

46 Genome Size Prokaryotes One circular chromosome ( Mb) Zero- many plasmids (1-1,000 Kb) Eukaryotes One nuclear genome, usually several chromosomes (10 Mb- 150 Gb) mitochondrial genomes (15-11,300 kb) chloroplast genomes in plants/algae ( kb)

47 Genome Size Prokaryotes One circular chromosome ( Mb) Zero- many plasmids (1-1,000 Kb) Eukaryotes One nuclear genome, usually several chromosomes (10 Mb- 150 Gb) mitochondrial genomes (15-11,300 kb) chloroplast genomes in plants/algae ( kb)

48 Genome Size Eukaryotes

49 Genome Size Eukaryotes mimiviruses

50 Some giant viruses are infected by other viruses! Giant viral genomes

51 Gene number and genome size in prokaryotes

52 Gene number and genome size in eukaryotes Protein- coding 21,000 21,000 28,000

53 The non- coding DNA of eukaryonc nuclear genomes Non-coding DNA: introns intergenic regions centromeric regions telomeric regions Most non-coding DNA is formed by identical or nearly identical repeated units (repetitive DNA) - two types of repetitive DNA: Tandem repeats (e.g. satellite DNA at centromeres and telomeric repeats at telomeres) Interspersed repeats (mostly transposable elements or TEs)

54 Differences in amount of repejjve DNA (TEs) explain differences in genome size in eukaryotes Mb 3000 Genomic DNA TE DNA Protein-coding DNA

55 ComparaNve genomics The study of the relanonship of genome structure and funcnon across different biological species or strains - Improve gene annotanon - IdenNfy funcnonal (conserved) sequences (genes, regulatory sequences, etc.) - Recognize species- specific features (novel genes, genomic rearrangements) - Describe the evolunon of genes and other funcnonal sequences and possibly how this relates to phenotypic evolunon - Improve our esnmates of fundamental genenc paramenters, i.e.: subsntunon rates - Obtain be\er phylogenenc trees of living organisms

56 Genome projects (not viruses, organelles or plasmids) (Jan 2015) complete and ongoing genome projects # species 1118 PopulaJon genomics: Thousands genomes/species 45, h\p://