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Plant Genomes

Plant Genomes. Houses of genetic materials. Total genetic material within a cell Usually referred to a haploid cell [Basic set of genetic material (1x)]. Plant Genomes. General perception: DNA in Nucleus Other organelles: Mitochondria / Chloroplast

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Plant Genomes

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  1. Plant Genomes Houses of genetic materials Total genetic material within a cell Usually referred to a haploid cell [Basic set of genetic material (1x)]

  2. Plant Genomes General perception: DNA in Nucleus Other organelles: Mitochondria / Chloroplast May not correlate with chromosome / gene number Extensive transfer of genes from organelles to nucleus

  3. Plant Genomes

  4. C value: DNA amount in nucleus of gamete (1 n) identified by flow cytometry Diploid (2n=2x) C value = genome size C value of polyploid >genome size (how?) For comparative study Nuclear genome

  5. Typical C value bacteria 1.5 * 107 bp mammals 1-2 * 109 bp spore-bearing vascular plants 50 * 109 bp gymnosperm 70 * 109 bp angiosperm 5-30 * 109 bp

  6. Typical C value Highly varied C value in plant Plants in general with big genome Variation of DNA amounts among closely related plants

  7. Orchidaceae C value Oncidium 0.6 pg Cypripedium 38.83 pg Paphiopedilum exul 16.5 pg Paphiopedilum dianthum 35.9 pg 109 bp = 1 pg

  8. Nuclear genome ? Increased genome size = Increased gene number Non-coding DNA regions: Variation in genome size

  9. Nuclear genome Diversity: as a result of nt change 0.1% every 2 * 105 years more diverse in non genic area why?

  10. Gene evolution Major rearrangement by Recombination duplication or deletion or transpose Exons and Regulatory elements shuffled as separate modules resulting in new proteins / new roles

  11. Gene evolution Minor change by Point Mutation following duplication replication errors of copies May result in related/unrelated gene products share common amino acid segments different functions

  12. Composition of nuclear genome Unique sequence low copy number mostly genes Repetitive sequence satellite DNA transposable element

  13. ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT Satellite DNA Minor component in density gradient Tandem repeats of simple sequence 1/3 of genome / in general not transcribed microsatellite / minisatellite / satellite 1 repeating unit: 1-2 nt / several thousands

  14. Satellite DNA Individual variation: different numbers of repeat (AAT)n(AT)m (AACATAGAAT)n (378 bp sequence)n 90% AAGAG and 10% AAGAGAG

  15. Transposon Transposable element / Transposition / Transpose Movable segment of DNA: interspersed / scattered in nuclear genome DNA element: transposase RNA intermediate: reverse transcriptase

  16. Genome organization Short Period Interspersion 1-2 kbp of unique DNA 0.3-1 kbp of repeated DNA most higher eukaryotes, esp with large genome Long Period Interspersion

  17. Genome organization Short Period Interspersion Long Period Interspersion alternated stretches of unique / repeated DNA longer than 10 kbp found in some eukaryotes with small genome size

  18. Co-linearity Organization of genomes of related plants Rice Maize Sorghum Wheat extensive co-linearity simple intrachromosomal inversion interchromosomal translocation Tomato Potato conserved gene copy number conserved gene order Tomato Pepper conserved gene repertoire highly divergent gene order

  19. Organelle Genome Mitochondria / Chloroplast Small and simple DNA Usually circular Multiple copies Clusters in matrix / stroma

  20. Organelle Genome Transcription / Translation in organelles Required > 90 nuclear-encoded proteins e.g. DNA polymerase RNA polymerase RNA processing enzyme

  21. Protein transport Unidirectional: cytosol to organelle (mt / ct) Signal: at N terminal as precursor sequence Transit peptide: about 4 kD uptake require energy unlinked translation and transport

  22. Organelle Genome Isolated organelles Continue to make DNA / RNA / Protein for a brief period Complete genetic system

  23. Mitochondrial genome Purple photosynthetic bacteria w/o PS ability Bacteria with oxidative phosphorylation Plant: largest mt genome more complicated than mt from animal, fungus or algae

  24. Mitochondrial genome Small animal 15-16 kbp Fungus / Algae 20-100 kbp Plant 150-2500 kbp

  25. Mitochondrial genome Plant mt genome: large and variable but encode only a few more proteins Oenothera 195 kbp Turnip 218 kbp Corn 570 kbp Muskmelon 2400 kbp

  26. Mitochondrial genome Organism Genome size Gene number Arabidopsis 367 kbp 58 Liverwort 184 kbp 66 Green algae 58 kbp 63 No correlation

  27. Plant mt genome Structure of plant mt genome Circular or linear or supercoiled Multipartite organization several molecules of different sizes Introns in some genes of some species

  28. Plant mt gene product Genetic apparatus rRNA, tRNA, rProtein Respiratory chain complex (energy metabolism) eg subunits I and II of Cytochrome c Oxidase ATPase subunits NADH dehydrogenase subunits

  29. Mitochondrial genome

  30. Mitochondria genetic map

  31. Mitochondria genetic map

  32. Mitochondria genetic map

  33. Mitochondrial genes Cytoplasmic inheritance Maternal / Uniparental inheritance

  34. Genome size expansion Flowering plant mt Large intron Sequence duplication DNA of virus origin Additional genes Intergenic unknown origin Human mt no intron Fungal mt with intron

  35. Arabidopsis mt Genome protein-coding genes 16.1 % introns 8.8 % ORF 10.2 % repetitive sequence 6.8 % tRNA 0.4 %

  36. Arabidopsis mt Genome rRNA 1.3 % nuclear-mt homologies 2.2 % nuclear origin 4.0 % plastid origin 1.2 % unaccounted for 49 %

  37. Chloroplast genome Photosynthetic cyanobacteria Similar sequence, size, structure, organization among organisms Differences in higher plant ct genomes accounted for by inverted repeats

  38. Chloroplast genome

  39. Chloroplast genome

  40. Plant chloroplast genome 100-120 genes ~ 20 genes with introns 2/3 maternal inheritance some biparental (pollen grain with ct)

  41. Plant chloroplast genome Colinearity found in maize, petunia spinach, cucumber and mungbean Extensive rearrangement in pea and broadbean

  42. Chloroplast Genome Chloroplast ribosome different from rbs in cytoplasm similar to rbs from E. coli structure / nt sequence antibiotic sensitivity

  43. Chloroplast Genome Basic regulatory sequences (promoter / terminator) similar to bacterial genome

  44. Chloroplast DNA Structure Circular or supercoiled About 125-200 kbp Single copy / inverted repeat regions Low GC content (rich / poor regions) Most genes: polycistronic (except for rbcL)

  45. Chloroplast genome

  46. Chloroplast genes Function: photosynthesis, fatty acid synthesis nitrogen metabolism and sulfate reduction Encode: Translation component tRNA rRNA rProtein Subunits of transcription Subunits of photosynthetic enzymes

  47. Spinach ct genome Double-stranded circular 150 kbp 108 unique loci with know functions 17 genes with intron quadripartite

  48. Spinach ct genome 2 inverted repeats of about 25 kbp 2 single-copy regions (large and small) RNA genes Protein genes

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