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Genome Evolution Chromosomes Heslop-Harrison ICC Prague

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Pat Heslop-Harrison presentation for International Chromosome Conference Prague September 2018 Meiosis, recombination, pairing, mitochondria, evolution, genomics, oligonucleotides, in situ hybridization, breeding, genetics, cytogenetics, ICC, ICC22

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Genome Evolution Chromosomes Heslop-Harrison ICC Prague

  1. 1. Chromosome and Genome Evolution in Plants and Animals Pat Heslop-Harrison Twitter: @PatHH1 #ICC22 Slideshare: PatHH1 www.molcyt.com phh@molcyt.com International Chromosome Conference Prague 2-5 September 2018
  2. 2. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  3. 3. Wheat evolution and hybrids Triticum uratu 2n=2x=14 AA Einkorn Triticum monococcum 2n=2x=14 AA Bread wheat Triticum aestivum 2n=6x=42 AABBDD Durum/Spaghetti Triticum turgidum ssp durum 2n=4x=28 AABB Triticum dicoccoides 2n=4x=28 AABB Aegilops speltoides relative 2n=2x=14 BB Triticum tauschii (Aegilops squarrosa) 2n=2x=14 DD Triticale xTriticosecale 2n=6x=42 AABBRR Rye Secale cereale 2n=2x=14 RR
  4. 4. green plants land plants vascular plants seed plants flowering plants diversification of angiosperms ANA ε Ginkgo Taxus Pinus Cedrus Sequoia Welwitschia Ephedra Lycophytes (ca. 1200 species) Physcomitrium sp. Chlorophytes (ca. 4300 species) 0100200300400 Mya500 AGF Charophytes (ca. 12,000 species) Sphagnum sp. Physcomitrella Monilophytes (ca. 13,000 species) Vitis (grapevine) Solanum (tomato, potato) Arabidopsis Carica (papaya) Populus (poplar) Linum (flax) Brassica (rapeseed) Glycine (soybean) Malus (apple) Musa (banana) Oryza (rice) Triticum (wheat) Zea (maize) β α γ ρσ τ Nicotiana (tobacco) Petunia ζ Bryophytes (20,000 spp) Gymnosperms (1000 spp) Green algae ‘Pteridophytes’ Angiosperms (400,000 spp) Eudicots Monocots Basal Angiosp. Karine Alix, Schwarzacher, HH, Ann Bot 2017
  5. 5. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  6. 6. 4D T4DL*4Ai#2S DAPI Afa Thin all (blue) (green) (red) rye Th. intermedium (Thin) Heterochromatin (hybridizes with genomic rye and Th. intermedium DNA pSc119.2/variabl e between lines 5S rDNA 45S rDNA dpTa1/Afa T1BL*1RS BP III 1B recombinant BPI and BPII Thin (red) 5S 45S 119.2 (green) 45S (red) pSc119.2 (green) Thin (red) 5S (green) Thin (red) 119.2 (green) 1B Th. intermedium DNA pSc119.2/CS13 Ali N, PHH et al. Heredity 2016
  7. 7. NO2Y5149 Mace Tomahawk Wheat Streak Mosaic Virus resistance From Thinopyrum sp in wheat
  8. 8. Patokar C, PHH et al. Chromosoma 2016
  9. 9. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  10. 10. Recombination in alien fragments Th. intermedium DNA-green AfaThin-red NiazAli Meiosis and chromosome pairing in hexaploid wheat
  11. 11. Interphase Leptotene Early ZygoteneCENH3TRSDAPICENH3ASY1CENH3ASY1 Centromere dynamics and timing of chromosome synapsis (6x wheat) Adel Sepsi, Higgins, HH, Schwarzacher. Dynamic progression through meiosis in hexaploid wheat. Plant Journal 2017 ImmunoFISH for insight into meiotic processes in nuclei of grasses Adel Sepsi, HH, Schwarzacher et al. Frontiers in Plant Science 2018
  12. 12. Centromere dynamics and timing of chromosome synapsis (6x wheat) Sepsi et al. Plant Journal 2017 0 5 10 15 20 25 30 35 40 Interphase Leptotene Early Mid-late Pachytene Diplotene Zygotene Zygotene 2n=42 3 x 14 chromosomes 21 bivalents 3 x 7 pairs of chromosomes
  13. 13. Mid Zygotene Pachytene DiploteneEarly Zygotene Dynamic of centromeres during meiosis Sepsi A, Higgins JD, Heslop-Harrison JS and Schwarzacher T, 2017. CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat Plant Journal 89: 235-249 doi: 10.1111/tpj.13379 CENH3 centromere ASY1 associated with the lateral elements (unpaired) ZYP1 central element of the synaptonemal complex (paired)
  14. 14. YouTube pathh1 – meiosis https://www.youtube.com/watch?v=8lBdErxq2Kk Zygotene and Initiation of synapsis: short, linear paired SC (synaptonemal complex, purple, anti-ZYP1) stretches at the telomere pole opposite to the centromeres (red, anti-CENH3): ZYP1 polymerization starts from subtelomeric regions
  15. 15. Mid Zygotene Pachytene DiploteneEarly Zygotene Dynamic of centromeres during meiosis
  16. 16. Mid Zygotene Pachytene DiploteneEarly Zygotene Dynamic of centromeres during meiosis
  17. 17. (a) (b) (c) (d) (e) (f) (g) (h) (i) ASY1CENH3DAPI
  18. 18. (b) Centromere depolarisation and SC formation during Zygotene Interphase Leptotene Zygotene Late ZygoteneTelomere bouquet Homologue chromosome pairs Centromeres ZYP1 Early Zygotene 1 2 3 Subtelomeric synapsis Interstitial alignment Interstitial elongation (a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I. Sepsi et al. Plant Journal 2017
  19. 19. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  20. 20. B. nigra BB 2n=2x=16 760Mbp B. rapa AA 2n=2x=20 564Mbp B. juncea AABB 2n=4x=36 1495Mbp B. carinata BBCC 2n=4x=34 1544Mbp B. oleracea CC 2n=2x=18 760Mbp B. napus AACC 2n=4x=38 1324Mbp
  21. 21. Genome Specificity of a CACTA (En/Spm) Transposon – Karine Alix et al. B. napus (AACC, 2n=4x=38) – hybridized with C-genome CACTA element red B. oleracea (CC, 2n=2x=18) B. rapa (AA, 2n=2x=20)
  22. 22. Genome Specificity of a CACTA (En/Spm) Transposon AJ 245479 AC 189496 AC 189446 AC 189655 AC 189480 Bot1-1 Bot1-2 Bot1-3 large insertion specific of Bot1-1 Bo6L1-15 1010bp large insertion in common between Bot1-2 and Bot1-3 Rearrangement specific of Bot1-3 B. napus B. rapa B. oleracea AJ 245479 AC 189496 AC 189446AC 189446 AC 189655AC 189655 AC 189480AC 189480 Bot1-1Bot1-1 Bot1-2Bot1-2 Bot1-3Bot1-3 large insertion specific of Bot1-1 Bo6L1-15 1010bp large insertion in common between Bot1-2 and Bot1-3 Rearrangement specific of Bot1-3 B. napus B. rapa B. oleracea
  23. 23. Sequences of chr A9 Brassica rapa vs chr C8 Brassica oleracea
  24. 24. • FROM • Feng Cheng, Jian Wu & Xiaowu Wang. Genome triplication drove the diversification of Brassica plants • Horticulture Research 1, Article number: 14024 (2014)
  25. 25. Massive oligonucleotide pools – >20,000 c. 50-mers = >1,000,000 bp • Designed along chromosome sequence, then screened to remove sequences that have homology to other sites or repetitive DNA
  26. 26. Probe pools to single-copy sequence, unique locations within 500kb bands on selected A genome chromosomes. Most (pie area is proportional to oligo numbers) mapped to bands on B and C genome chromosomes. Neha Agrawal
  27. 27. Oligo pool Brassica rapa AA 2 pairs both ends 2 pairs one end Neha Agrawal 2019
  28. 28. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  29. 29. Illumina survey sequence of 5 animals • Sarbast Mustafa • In: Mitochondrial DNA part A 2018 Hamdani Karadi
  30. 30. HA HB HD HC HE
  31. 31. New mitochondrial assemblies compared with the nuclear chromosome assemblies (Ovis aries Oar_v4.0)
  32. 32. 16S rRNA CYTB CDS (1036bp)Control region ND1
  33. 33. Numts – nuclear-mitochondrial sequences De novo assembly of variant mitochondrial sequences Blasting against NCBI Assemblies of variant reads: homology to mitochondria of Ovis canadensis, O. ammon, O. vignei, genus Capra A few regions reported as nuclear including to O. canadensis chromosome 26, O. aries chromosome X
  34. 34. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  35. 35. Organelle sequences from chloroplasts or mitochondria Sequences from viruses Transgenes introduced with molecular biology methods Genes, regulatory and non- coding low-copy sequences Dispersed repeats Repetitive DNA sequences Nuclear Genome Tandem repeats Satellite sequences DNA transposonsRetrotransposons Centromeric repeats Structural components of chromosomes Telomeric repeats Simple sequence repeats or microsatellites Repeated genes Subtelomeric repeats 45S and 5S rRNA genes Blocks of tandem repeats at discrete chromosomal loci DNA sequence components of the nuclear genome After Assunta Biscotti et al. Chromosome Research 2015 Other genes Transposable elements Autonomous/ non-autonomous ? PADS – Passively amplified DNA sequences ?
  36. 36. Repeats and diversity in sheep - 2n=54 Major tandemly repeated sequences SatI and SatII at many centromeres Sex chromosomes are different to autosomes X Y Chromosome Research: special issue on repetitive DNA December 2015 Cover Sarbast Mustafa et al.
  37. 37. Repeats in sequence reads •SatI: 816bp monomer, 6% of genome •SatII: 702bp monomer, c. 1.6% of genomeSatellite I Satellite II
  38. 38. Satellite I SCP1 Satellite II Clusters at centromeres Schwarzacher et al. 2019
  39. 39. SCP1 Telo SatI SCP1 Sat I SatII OAR2 DOMESTIC SHEEP OVIS ARIES (OAR, 2n=54)
  40. 40. METACENTRIC GC- rich centromeric heterochromatin • Mc1-Al: present in all metacentric chromosomes (SSC1 – SSC12 and X ) • Mc1-Av: present only in SSC1 • Mc1-Pv: present on SSC10, 11 and 12 ACROCENTRIC AT-rich centromeric heterochromatin • Ac2-3.4: present in all acrocentric chromosomes (SSC13-18); • Ac2-3.5: present in all acrocentrics (SSC13-SSC18) KARYOTYPE OF THE DOMESTIC PIG SUS SCROFA DOMESTICA (SSC; 2n = 38) Michael Jantsch, Vienna
  41. 41. (Schwarzacher et al., 1984; Jantsch et al., 1990). METACENTRIC GC- rich centromeric heterochromatin • Mc1-Al: present in all metacentric chromosomes (SSC1 – SSC12 and X ) • Mc1-Av: present only in SSC1 • Mc1-Pv: present on SSC10, 11 and 12 ACROCENTRIC AT-rich centromeric heterochromatin • Ac2-3.4: present in all acrocentric chromosomes (SSC13-18); • Ac2-3.5: present in all acrocentrics (SSC13-SSC18) Michael Jantsch, Vienna KARYOTYPE OF THE DOMESTIC PIG SUS SCROFA DOMESTICA
  42. 42. XY Sus scrofa domestica Immuno-Staining and FISH SSC1 SSC1 SCP1 Mc1-Av Ac2-3.5 Mc1-Av Dafria. Tekiner, Schwarzacher
  43. 43. SSC1 Ac Ac Ac Ac Ac Ac SCP1 Ac2-3.5 SCP1 telomere Sus scrofa domestica Immuno-Staining and FISH The acrocentric heterochromatin forms a tight DAPI positive chromocentre at pachytene . The repetitive sequences of the six acrocentric bivalents join together into one or sometimes two large areas . The SCs are however not associated themselves or directly via their telomeres Pachytene Conventional spread DAPI staining SC Schwarzacher, Dafria and Akdeniz
  44. 44. X X Mc1-Al Ac2-3.4 SCP3 Ac2-3.5 Mc2-Al Acrocentric heterochromatin associates Metacentric heterochromatin is dispersed Sus scrofa domestica Immuno-Staining and FISH Schwarzacher and Akdeniz
  45. 45. How do genomes evolve? •Polyploidy / whole genome duplication •Translocations / rearrangements •Aneuploidy •Recombination •Repetitive DNA & genome size •Cytoplasm-nuclear transfer
  46. 46. Dr Mark Goodwin (195/6?-2018)
  47. 47. Fundamental properties of a genome • DNA sequence (example: GTGTCACT…) • Genome size (eg 2,000 Mbp) • Chromosome number (eg 2n = 24) • Ploidy (eg 2n = 8x) • Chromosome morphology • Repetitive DNA nature and content BUT … does it matter? can they be exploited or used?
  48. 48. Nothing special about crop genomes? Crop Genome size 2n Ploidy Food Rice 400 Mb 24 2 3x endosperm Wheat 17,000 Mbp 42 6 3x endosperm Maize 950 Mbp 10 4 (palaeo- tetraploi d) 3x endosperm Rapeseed Brassica napus 1125 Mbp 38 4 Cotyledon oil/protein B. oleracea Cabbage etc 488 Mbp 18 2 Leaf/flower/bud/root Cassava 770 Mbp 36 2 Tuber Soybean 1,100 Mbp 40 4 Seed cotyledon Oil palm 1,800 Mbp 32 2 Fruit mesocarp Banana 540 Mbp (x) 33 3 Fruit mesocarp Heslop-Harrison & Schwarzacher 2012. Genetics and genomics of crop domestication. In Altman & Hasegawa Plant Biotech & Agriculture. Tinyurl.com/domest … and crops are ‘random’ subset of all genomes
  49. 49. Chromosome and Genome Evolution in Plants and Animals Pat Heslop-Harrison Twitter: @PatHH1 #ICC22 Slideshare: PatHH1 www.molcyt.com phh@molcyt.com International Chromosome Conference Prague 2-5 September 2018

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