1. Genomes

2. Definition Complete set of instructions for making an organis Master blueprints for all enzymes, cellular structures & activities An organism‘s complete set of DNA All the DNA contained in the cell of an organism The collection of DNA that comprises an organism. Total genetic information carried by a single set of chromosomes in a haploid nucleus

3. Genome size

4. Plant DNA viruses are rare Cauliflower mosaic virus Spherical, kills Cauliflower and Brussel Sprouts Most plant viruses are small and comprised of ssRNA   Rod shaped, attacks tomato, pepper, beets, turnips, tobacco   2,130 identical proteins surround the ssRNA   ~10,000bp, ~10 genes Plant Viroids Plant Viruses

5. Highly complementary circular ssRNA No protein coat Smaller than viruses (few hundreds of bases) Smallest known virus is 3.2 kbp in size RNA does not code for any known protein Some even lack the AUG initiation codon Replication mechanism is unknown Viroids cannot recognize and infect host cell Relies on cells being weak or injured Proposed that viroids are "escaped introns" Viroids are usually transmitted by seed or pollen Infected plants can show distorted growth The first viroid to be identified was the Potato spindle tuber viroid (PSTVd) Some 33 species have been identified Plant Viroids

6. Procaryotic genomes Generally 1 circular chromosome (dsDNA) Usually without introns Relatively high gene density (~2500 genes per mm of E. coli DNA) Often indigenous plasmids are present 1.Eschericia coli 2.Agrobacterium tumefaciens

7. Eschericia Coli genome Single chromosome of approximately 5 million base pairs (5 Mbp) 4288 protein coding genes: Average ORF 317 amino acids Average gene size 1000 bp Very compact: average distance between genes 118bp Contour length of genome: 1.7 mm It can accept foreign DNA derived from any organism Some genes are arranged in the plasmid

8. Agrobacterium tumefaciens genome Genome size (chromosome) is aboutGenome size (chromosome) is about 6 Mb A large (~250kbp) plasmid called Tumor-inducing (Ti) plasmid)A large (~250kbp) plasmid called Tumor-inducing (Ti) plasmid) Plasmid contains genes responsible for the diseasePlasmid contains genes responsible for the disease Portion of the Ti plasmid is transferred between bacterial cells and plant cells  T-DNA (Transfer DNA)Portion of the Ti plasmid is transferred between bacterial cells and plant cells  T-DNA (Transfer DNA) T-DNA integrates stably into plant genomeT-DNA integrates stably into plant genome Single stranded T-DNA fragment is converted to dsDNA fragment by plant cellSingle stranded T-DNA fragment is converted to dsDNA fragment by plant cell Then integrated into plant genome Then integrated into plant genome 2 x 23bp direct repeats play an important role in the excision and integration process 2 x 23bp direct repeats play an important role in the excision and integration process

9. Plasmids Naturally Extra chromosomal circular DNAs They exist separate from the main chromosome They replicate within the host cells Their size vary form ~ 1,000 to 250,000 base pairs They can be divided into two broad groups according to how tightly their replication in regulated: 1. stringent plasmids (low copy number plasmids: 1-2 plasmids/cell) only replicate along with the main bacterial chromosome and so exist as single copy, or at most several copies within the cell 2. Relaxed plasmid (multi copy number plasmids) replicate autonomously of the main chromosome and have copy numbers of 10 - 500 per cells

10. Genome of diploid Saccharomyce cerevisiae cell Characteristic Chromosomes Plasmid Mitochondiral Relative amount (%)85510 Number of copies2 x 1660-100~50 (8-130) Size (kbp)14.000 6,318 70-76 Yeast genome

11. The yeast genome S. cerevisiae contains a haploid set of 16 well-characterized chromosomes, ranging in size from 200 to 2,200 kb Total sequence of chromosomal DNA is 12,8 Mb 6,183 ORFs over 100 amino acids long First completely sequenced eukaryote genome Very compact genome: Short intergenic regionsShort intergenic regions Scarcity of intronsScarcity of introns Lack of repetitive sequencesLack of repetitive sequences Strong evidence of duplication: Chromosome segmentsChromosome segments Single genesSingle genes Redundancy: non-essential genes provide selective advantage Redundancy: non-essential genes provide selective advantage

12. Plant genomes Plant contains three genomes Plant contains three genomes Genetic information is divided in the chromosome. Genetic information is divided in the chromosome. The size of genomes is species dependent The size of genomes is species dependent The difference in the size of genome is mainly due to a different number of identical sequence of various size arranged in sequence The difference in the size of genome is mainly due to a different number of identical sequence of various size arranged in sequence The gene for ribosomal RNAs occur as repetitive sequence and together with the genes for some transfer RNAs in several thousand of copies The gene for ribosomal RNAs occur as repetitive sequence and together with the genes for some transfer RNAs in several thousand of copies Structural genes are present in only a few copies, sometimes just single copy. Structural genes encoding for structurally and functionally related proteins often form a gene family Structural genes are present in only a few copies, sometimes just single copy. Structural genes encoding for structurally and functionally related proteins often form a gene family The DNA in the genome is replicated during the interphase of mitosis The DNA in the genome is replicated during the interphase of mitosis

14. Peculiarities of plant genomes Huge genomes reaching tens of billions of base pairs Huge genomes reaching tens of billions of base pairs Numerous polyploid forms Numerous polyploid forms Abundant (up to 99%) non coding DNA which seriously hinders sequencing, gene mapping and design of gene Abundant (up to 99%) non coding DNA which seriously hinders sequencing, gene mapping and design of gene Poor morphological, genetics, and physical mapping of chromosomes Poor morphological, genetics, and physical mapping of chromosomes A large number of “small-chromosome” in which the chromosome length does not exceed 3 μm A large number of “small-chromosome” in which the chromosome length does not exceed 3 μm The number of chromosomes and DNA content in many species is still unknown The number of chromosomes and DNA content in many species is still unknown

15. Size of the genome in plants and human Genome Arabidopsis thaliana Zea mays Vicia faba Human Nucleus 70 Millions 3900 Millions 14500 Millions 2800 Millions Plastid 0.156 Millions 0.136 Millions 0.120 Millions Mitochondrion 0.370 Millions.570 Millions.290 Millions.017 Millions

16. Organisation of the genome into chromosome The nuclear genome is organized into chromosome The nuclear genome is organized into chromosome Chromosomes consist of essentially one long DNA helix wound around nucleosome Chromosomes consist of essentially one long DNA helix wound around nucleosome At metaphase, when the genome is relatively inactive, the chromosome are most condensed and therefore most easily observed cytologically, counted or separated At metaphase, when the genome is relatively inactive, the chromosome are most condensed and therefore most easily observed cytologically, counted or separated Chromosomes provide the means by which the plant genome constituents are replicated and segregated regularly in mitosis and meiosis Chromosomes provide the means by which the plant genome constituents are replicated and segregated regularly in mitosis and meiosis Large genome segments are defined by their conserved order of constituent genes Large genome segments are defined by their conserved order of constituent genes

17. Genome composition 1.Heterochromatin Darkly staining portions of chromosomes, believed due to high degree of coiling Darkly staining portions of chromosomes, believed due to high degree of coiling Non-genic DNA Non-genic DNA a. Centromere ~ “middle” of Chromosomes ~ “middle” of Chromosomes spindle attachment sites spindle attachment sites b. Telomeres 1. ends of chromosome 2. important for the stability of chromosomes tips. 2. Euchromatin Lightly staining portion of chromosomes Lightly staining portion of chromosomes It represents most of the genomes It represents most of the genomes It contains most of genes. It contains most of genes.

18. Ploidy and chromosome number OrganismPloidy Chromosome number Corn Diploid (2X) 20 Tomato 24 Arabidopsis 10 Potato Tetraploid (4X) 48 Wheat Hexaploid (6X) 42

19. Organization of Plant Genome Protein coding gene Protein coding gene P Portion of genome which encodes for most of the transcribed genes (Protein coding genes) Non coding gene Non coding gene 1. Intron 2. 2. Regulatory elements of genes 3. Multiple copies of genes, including pseudogenes 4. Intergenic sequences 5. Interspersed repeats

20. Organization of Plant Genome Most plants contain quantities of DNA that greatly exceed their needs for coding and regulatory functions Very small percentage of the genome may encode for genes involved in protein production Based on kinetics: Low-copy-number DNA Low-copy-number DNA DNA sequences DNA sequences encodes for most of the transcribed genes (Protein coding genes) Medium-copy-number DNA Medium-copy-number DNA DNA sequences that encode ribosomal RNA (Tandemly repeated expressed DNA) High-copy-number DNA High-copy-number DNA I t is composed of highly repetitive sequences (Repetitious DNA)

21. Gene classification coding genes non-coding genes Messenger RNA Proteins Structural RNA Structural proteinsEnzymes transfer RNA ribosomal RNA other RNA Chromosome (simplified) intergenic region

22. Protein Coding Genes Segment of DNA which can be transcribed and translated to amino acid

23. Protein Coding Genes Plant contains about 10 000 – 30 000 structural genes Plant contains about 10 000 – 30 000 structural genes They are present in only a few copies, sometimes just one (single copy gene) They are present in only a few copies, sometimes just one (single copy gene) They often form a gene family They often form a gene family The transcription of most structural genes is subject to very complex and specific regulation The transcription of most structural genes is subject to very complex and specific regulation The gene for enzymes of metabolism or protein biosynthesis which proceed in all cells are transcribed more often The gene for enzymes of metabolism or protein biosynthesis which proceed in all cells are transcribed more often Most of the genes are switched off and are activated only in certain organ and then often only in certain cells Most of the genes are switched off and are activated only in certain organ and then often only in certain cells Many genes are only switched on at specific times Many genes are only switched on at specific times House keeping gene: The genes which every cell needs for such basic functions independent of its specialization

24. What do the genes encode? Genes for basic cellular functions such as translation, transcription, replication and repair share similarity among all organisms Basic functions Yeast – simplest eukaryote Worm – programmed development Fly – complex development Arabidopsis – plant life cycle + Microbes highly specialized Gene families expand to meet biological needs.

25. Plant genome sizes

26. Small difference in gene number, although rice genome is 3x the size Predicted Gene numbers

27. How to study Genome? Genomics

28. 21 st century Biology: integration