Genomes & Genome evolution

1. Genomes & Genome evolution

2. Genomes and Genome Evolution - BIOL 4340/6301What to expect and some suggestions. • I like think of myself as fair but reasonably tough • I want people to do well but I’m not willing to compromise on the material or ethical guidelines to make it happen. • There is no extra credit. This is non-negotiable. • Study for the exams, do the assignments, and do well on both. • Ask questions IN CLASS • Makes things more interesting for me • You will do better on the exams and assignments the more you talk and think about the material • Others probably have the same question • You’re paying, get your money’s worth • Interactions with other humans tends to wake people up • Office hours!!!!!!!!!! I have them. Take advantage. • I am an evolutionary biologist. This class is taught from an evolutionary perspective. • Because of my research interests, I tend to focus on animals. Please help me to avoid that bias.

3. Genomes and Genome Evolution - BIOL 4301/6301What to expect and some suggestions. • Absorb and critique anything related to the subject. This includes but is not restricted to: • Popular news articles, TV shows (CSI, Bones, etc.), textbooks, wikipedia, etc. Genomics is everywhere. • Bring in what you find for discussion. • One good source - https://geneticliteracyproject.org/ • Website - http://davidraylab.com • Again, ask questions during class • Ask questions DURING CLASS • Did I mention that you should ask questions during class? • You WILL see pictures of my adorable children and beautiful wife. This is also non-negotiable.

5. Course Objectives and Assumptions • Objectives: By the end of this course you should be able to… • describe the methods and principles of modern genome analysis • explain the basic techniques of genome sequencing and analysis • perform basic genome assemblies and some basic genome analyses using common software • describe the way genomes change over time • apply principles of genomics to modern biological questions • intelligently discuss the outcomes of a variety of genome projects

6. Course Objectives and Assumptions • Assumptions: I am assuming that you… • have a working knowledge of Mendelian genetics • have a working knowledge of DNA, RNA and proteins • understand the basic differences between eukaryotes and prokaryotes • have a basic understanding of the concept of a gene • have a working knowledge of the ‘central dogma’ of Biology • give a rat’s behind about learning this stuff

7. The Syllabus • Let’s go through the highlights • Read all of it, please

8. High Performance Computing • For parts of this class, you will be working on compute nodes at the TTU High Performance Computing Cluster (HPCC) • You will need an account. • Go to: http://www.depts.ttu.edu/hpcc/accounts/studentrequest.php • Agree to all policies • Fill in all necessary fields • Use me as your Faculty/Staff contact • David A Ray, david.a.ray@ttu.edu, 806-834-1677 • Complete this by August 31, 2019

9. Current Events Reminder/Example

10. Genome paper presentations • Friday manuscripts by grad students • I will provide the first example on Friday, cheetah manuscript • Genomic legacy of the African cheetah, Acinonyx jubatus • Graduate students are responsible for the remaining manuscripts throughout the semester • You can choose your own (with my approval) or I can choose for you • Option 1: Choose your own: • Option 2: I choose for you: • See next slides • Regardless, identify two choices by Monday of next week so I can generate a schedule

11. Genome paper presentations • Potential manuscripts • The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior - https://doi.org/10.1093/gbe/evz139 • Genome-wide SNP Data Reveal and Overestimation of Species Diversity in a Group of Hawkmoths - https://doi.org/10.1093/gbe/evz113 • Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponianippon) - https://doi.org/10.1093/gbe/evz149 • The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae - https://doi.org/10.1093/gbe/evz104 • Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection - https://doi.org/10.1093/gbe/evz099

12. Genome paper presentations • Potential manuscripts • Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum - https://doi.org/10.1093/gbe/evz087 • Epigenetic maintenance of topological domains in the highly rearranged gibbon genome – https://doi.org/10.1101/gr.233874.117 • The peopling of South America and the trans-Andean gene flow of the first settlers - https://doi.org/10.1101/gr.234674.118 • Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide - https://doi.org/10.1093/molbev/msz066 • Genomic Evidence of Local Adaptation to Climate and Diet in Indigenous Siberians - https://doi.org/10.1093/molbev/msy211 • L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis - https://doi.org/10.1101/gr.226993.117

13. Genome paper presentations • Potential manuscripts • Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae) - https://doi.org/10.1093/molbev/msz099 • Adaptation to Plant Communities across the Genome of Arabidopsis thaliana - https://doi.org/10.1093/molbev/msz078 • Genome Evolution of the Obligate Endosymbiont Buchneraaphidicola- https://doi.org/10.1093/molbev/msz082 • Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover - https://doi.org/10.1093/molbev/msz045 • Sequencing Disparity in the Genomic Era - https://doi.org/10.1093/molbev/msz117

14. Finally, what topics are you interested in? • Genomic impacts on medicine? • Genome engineering? • Modern genomic analysis? • History of genomics? • Genomic impacts on society? • Human genomics? • ….. Please let me know

15. Fundamental Concepts UNIT 1

16. Genome • Definition depends upon organism, organelle, or virus one is talking about • Generic definition: Minimum DNA complement that define an organism/organelle/virus • Organelles are not, in and of themselves, living creatures. Thus something can have a genome and not be “alive.” • Viruses may or may not be alive, depending upon how one defines life • The dead have genomes too.

17. Things with genomes Things without genomes • Dirt • Rocks • Water • Air • Fire • But even these things may be contaminated with genomic DNA (…well, maybe not fire) • Prokaryotes • Monera (bacteria) • Archaea • Mitochondria • Chloroplasts • Viruses • Eukaryotes • Animals • Plants • Fungi • Protists

18. What genomes can and can’t do • A genome constrains but does not dictate the features of an organism • Environmental impacts • Toxins, exercise, exposure to disease • Epigenetic impacts • If someone were to clone you…?

19. Genomics • Study of genomes? • Research in which robotics, automated sequencing, and advanced computational methods are utilized to rapidly and efficiently characterize genomes and their components

20. Nucleic Acids • Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) • Composed of chains of nucleotides (ribonucleotides for RNA, deoxyribonucleotides for DNA)

21. Nucleic Acids • Deoxyribonucleic acid • A polymer of nucleotides linked by phosphodiester bonds

22. Nucleic Acids • Purine vs. pyrimidine • Carbon positions

23. Nucleic Acids • Deoxyribonucleic acid • Antiparallel strands held together by hydrogen bonds • Strands are complementary

24. Scanning-tunneling electron micrograph DNA in 3D Pretty uncanny resemblance, don’t you think?

25. Nucleic Acids • Deoxyribonucleic acid can denature, renature & hybridize • Denaturation – separation of the double helix by the addition of heat or chemicals • Renaturation – the reformation of double stranded DNA from denatured DNA • The rate at which a particular sequence will reassociate is proportional to the number of times it is found in the genome • Given enough time, nearly all of the DNA in a heat denatured DNA sample will renature.

26. Nucleic Acids • Cot analysis represents the first real whole genome analyses • Cot = the initial DNA concentration (Co) x time (t)

27. Nucleic Acids • Ribonucleic acid • Ribose vs. deoxyribose • Thymine = 5 methyl-uracil • Usually single stranded

28. Nucleic Acids • Intramolecular base-pairing • Enhanced base-pairing capacity due to G:U bonding • Hairpins • Bulges • Loops • Stem-loop structures • Pseudoknots

29. Nucleic Acids • Complex tertiary structures • Much more flexible than DNA • Capable of triple bonds and base-backbone interactions • Often ‘molded’ by proteins and snoRNPs • Leads to complex 3° structures with catalytic capability - ribozymes

30. Nucleic Acids OH OH NB NB NB NB DNA RNA OH O OH OH P O C OH O P P P O O O C C C O OH OH

31. Replication • DNA is replicated in a semi-conservative fashion, i.e., each daughter molecule is composed of one strand of the original molecule and one newly synthesized strand. • DNA polymerase is the enzyme that catalyzes synthesis of new strands out of dNTPs.

32. Replication: Key points • DNA polymerase cannot generate a new strand without a 3’ OH on which to add a nucleotide. Primers are required. • New strands generated from 5’ to 3’. • Replication is bidirectional. Replication forks proceed from an initiation site in both directions. • Multiple sites of initiation are found along a chromosome. Initiation sites are often AT rich as AT base pairs are less stable and thus come apart more easily. • Okazaki fragments are generated along lagging strand. • http://www.johnkyrk.com/DNAreplication.html • http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

33. Current event • “At one extreme, you get papers which show that a variant of Gene X is common in a small group of people with Disease Y and not in healthy controls… and that’s it. You don’t really know if X is really responsible for Y, or even if the result is genuine and not a false alarm produced by small numbers.” • “At the other extreme, you have this—a study that used a smorgasbord of experiments to identify 18 new genes behind hereditary spastic paraplegias(HSPs).” • What is exome sequencing? How is it different from whole genome sequencing? • “They found 55 families with the disorders and sequenced every gene in 93 of their members. They identified several genes that seemed to cause HSPs in these people, and they bred mutant fish to check that getting rid of these genes actually does produce relevant symptoms. They created a network to show what these genes do, and how they interact with each other. And they used that network to find even more HSP genes.” • “the 18 new genes and the 22 old ones explain around 70 percent of the HSP cases among the team’s recruits.” • “The team then extended the network to look at other genes that interacted with the ones they identified—the “friends of friends”. ” https://www.nationalgeographic.com/science/phenomena/2014/01/30/now-this-is-how-you-find-disease-genes/

34. (A) HSP seeds + candidate network (edge-weighted force-directed layout), demonstrating many of the genes known to be mutated in HSP (seeds, blue) and new HSP candidates (red), along with others (circles) constituting the network. 

35. (A) HSP candidate genes predicted from the HSPome found mutated in the HSP cohort. BICD2, MAP, and REEP2 were subsequently found mutated in HSP families 1370 (B), 1226 (D), and 1967 (F), respectively. (C) Homozygosity plot from family 1370. Red bars, regions of homozygosity; arrow, homozygous block containing BICD2. (E) Linkage plot of family 1226; arrow, MAG locus. (G) Homozygosity plot; arrow, REEP2 locus. (H to J) Zoom in from HSPome for specific interaction identifying candidates CCDC64 (a paralog of BIC2D), MAG, and REEP2 (yellow) with previously published (blue) and newly identified (red) genes mutated in HSP. Blue lines denote manually curated interactions.

36. Genome paper presentations • Potential manuscripts • The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior - https://doi.org/10.1093/gbe/evz139Simrandeep • Genome-wide SNP Data Reveal and Overestimation of Species Diversity in a Group of Hawkmoths - https://doi.org/10.1093/gbe/evz113Megan • Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponianippon) - https://doi.org/10.1093/gbe/evz149Megan • The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae - https://doi.org/10.1093/gbe/evz104Aman • Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection - https://doi.org/10.1093/gbe/evz099

37. Genome paper presentations • Potential manuscripts • Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum - https://doi.org/10.1093/gbe/evz087 • Epigenetic maintenance of topological domains in the highly rearranged gibbon genome – https://doi.org/10.1101/gr.233874.117 • The peopling of South America and the trans-Andean gene flow of the first settlers - https://doi.org/10.1101/gr.234674.118Joanna • Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide - https://doi.org/10.1093/molbev/msz066 • Genomic Evidence of Local Adaptation to Climate and Diet in Indigenous Siberians - https://doi.org/10.1093/molbev/msy211Claudio • L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis - https://doi.org/10.1101/gr.226993.117

38. Genome paper presentations • Potential manuscripts • Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae) - https://doi.org/10.1093/molbev/msz099Joanna • Adaptation to Plant Communities across the Genome of Arabidopsis thaliana - https://doi.org/10.1093/molbev/msz078Minghao • Genome Evolution of the Obligate Endosymbiont Buchneraaphidicola- https://doi.org/10.1093/molbev/msz082 • Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover - https://doi.org/10.1093/molbev/msz045 • Sequencing Disparity in the Genomic Era - https://doi.org/10.1093/molbev/msz117

39. RNA • Normally single-stranded • Generated from NTPs by RNA polymerase using DNA as a template (transcription) • As with DNA replication, new strand assembled in 5’ to 3’ direction by phosphodiester bond formation • RNA is inherently less stable than DNA

40. Major types of RNA • Messenger RNA (mRNA) – carries genetic instructions (coded in DNA) from the nucleus into the cytoplasm. mRNA molecules are often called transcripts. • Ribosomal RNA (rRNA) – a structural component of ribosomes (the complexes that are involved in assembling proteins based upon information in mRNA templates) • Transfer RNA (tRNA) – acts as carrier of amino acids during protein assembly • Regulatory RNAs – Many groups; miRNAs, siRNAs, CRISPR RNAs, antisense RNAs, long non-coding RNAs

41. Transcription • Generation of an RNA strand from a DNA template • Much of the control over cell development comes at the transcriptional level – All somatic cells have same DNA but can differ tremendously in morphology and function • Differential gene expression

42. Transcription: Key points • Transcription starts at the promoter, a site along the DNA molecule where RNA polymerase binds. • RNA polymerase is recruited to the promoter by transcription factors. • New strand generated from 5’ to 3’. • Only one of the two DNA strands serves as a template(antisense strand). The other strand (sense strand) has the same sequence as the mRNA molecule except dTMPs have been substituted with UMPs. • Which stand is used as a template differs between genes. • After transcription, mRNA undergoes post-transcriptional modifications. Generally, a methyl-guanosine cap is added to the 5’ end and a tail of adenosine nucleotides (poly-A tail) is added to the 3’ end. • In eukaryotes, the mRNA undergoes post-transcriptional splicing – introns are removed and exons are spliced together.

43. Transcription: Key points • Precursor mRNA (pre-mRNA) or heterogeneous nuclear RNA (hnRNA): mRNA immediately after transcription and before post-transcriptional modification • Mature mRNA (or simply mRNA): Transcript after post-transcriptional modifications. • cDNA (complementary DNA): A DNA molecule generated in a reaction catalyzed by reverse transcriptase using mature mRNA as the template.

44. Transcription models • http://www.johnkyrk.com/DNAtranscription.html • http://www.dnalc.org/resources/3d/13-transcription-advanced.html

45. Laptop alert • Bring them on Wednesday • https://github.com/davidaray/Genomes-and-Genome-Evolution/wiki Blackboard page is active

46. rRNA • Associated with proteins to form ribosomes • Several different rRNAs • Genes that code for rRNA are typically referred to as rDNA sequences • rDNA sequences found in more or less tandem repeats in genome

47. tRNA • tRNA molecules deliver amino acids to ribosomes during protein synthesis (translation) • tRNAs have considerable secondary structure due to base pairing • Clover leaf 2D structure • L-shaped 3D structure • There are more than 20 tRNAs (i.e., there is some redundancy) • tRNA structure is highly conserved (e.g., human tRNAs can function in yeast)

48. Amino acids • Proteins are made of chains of amino acids • There are 20 amino acids utilized by biological systems • Each codon in mRNA represents an amino acid or a start/stop signal • Amino acids can be acidic (net negative charge), basic (positive charge), uncharged polar (ends have different net charges), and non-polar. • Uncharged polar, acidic, and basic amino acids tend to be hydrophilic and thus are often found on the outside of proteins. • Non-polar amino acids tend to be hydrophobic and thus are clustered in the middle of proteins.

49. Genetic code

50. Translation • Construction of an amino acid chain (protein) by a ribosome based upon the nucleotide sequence of a mRNA molecule • While there are minor differences between eukaryotic and prokaryotic translation processes, most steps in translation are well conserved. http://www.johnkyrk.com/DNAtranslation.html