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. Why can be in haploid nucleus?
What is haploid nucleus?

4. Genome size

5. Plant Viruses 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

6. Plant Viroids 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

7. Procaryotic genomes Eschericia coli 2. Agrobacterium tumefaciens
Most have a single, double-stranded circular DNA molecule
Usually without introns
Since there is no nucleus, the DNA floats freely within the cell
Proteins cause the DNA to coil tightly forming a nucleoid region
Relatively high gene density
Often indigenous plasmids are present
Eschericia coli Agrobacterium tumefaciens

8. 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

9. Agrobacterium tumefaciens genome
Genome size (chromosome) is about 6 Mb
A large (~250kbp) plasmid called Tumor-inducing (Ti) plasmid)
Plasmid contains genes responsible for the disease
Portion of the Ti plasmid is transferred between bacterial cells and plant cells  T-DNA (Transfer DNA)

10. Bacterial plasmid

11. Naturally Extra chromosomal circular DNAs
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 replicate autonomously (origin of replication)
They may contain resistance genes
They may be transferred from one bacterium to another
They may be transferred across kingdoms
Plasmids may be incompatible with each other
Plasmids are circular double stranded DNA
Plasmids can be cleaved by restriction enzymes, leaving sticky ends
Artificial plasmids can be constructed by linking new DNA fragments to the sticky ends of plasmid

12. Fungal genomes: S. cerevisiae
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 regions
Scarcity of introns
Lack of repetitive sequences
Strong evidence of duplication:
Chromosome segments
Single genes
Redundancy: non-essential genes provide selective advantage

13. Genome of diploid Saccharomyce cerevisiae cell
Yeast genome
Genome of diploid Saccharomyce cerevisiae cell
Characteristic Chromosomes Plasmid Mitochondiral
Relative amount (%)
Number of copies 2 x ~50 (8-130)
Size (kbp) ,

14. Plant genomes Plant contains three genomes
Genetic information is divided in the chromosome.
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 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
The DNA in the genome is replicated during the interphase of mitosis

16. Peculiarities of plant genomes
Huge genomes reaching tens of billions of base pairs
Numerous polyploid forms
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
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

17. Size of the genome in plants and human
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

18. Organisation of the genome into chromosome
The nuclear genome is organized into chromosome
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
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

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

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

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

22. 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
DNA sequences encodes for most of the transcribed genes (Protein coding genes)
Medium-copy-number DNA
DNA sequences that encode ribosomal RNA (Tandemly repeated expressed DNA)
High-copy-number DNA
It is composed of highly repetitive sequences (Repetitious DNA)

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

24. Segment of DNA which can be transcribed and translated to amino acid
Protein Coding Genes
Segment of DNA which can be transcribed and translated to amino acid 40

25. Protein Coding Genes House keeping gene:
Plant contains about – structural genes
They are present in only a few copies, sometimes just one (single copy gene)
They often form a gene family
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
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
Yeast, ~1% of genes have ORFs<100 aa
House keeping gene:
The genes which every cell needs for such basic functions independent of its specialization

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

27. Plant genome sizes 27

28. Predicted Gene numbers
Small difference in gene number, although rice genome is 3x the size 28 28

29. How to study Genome?
Genomics

30. 21st century Biology: integration