 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

 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

 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



Most have a single, doublestranded 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
1. Eschericia coli 2. Agrobacterium tumefaciens


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

 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)

 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

 S. cerevisiae contains a haploid set of 16 wellcharacterized 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

Characteristic
Relative amount (%)
Number of copies
Size (kbp)
Chromosomes Plasmid
85 5
Mitochondiral
10
2 x 16 60-100 ~50 (8-130)
14.000 6,318 70-76

 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

 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

Genome
Nucleus
Arabidopsis thaliana
Zea mays Vicia faba Human
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

 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

1. Heterochromatin
 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 .

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

 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

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
I t is composed of highly repetitive sequences (Repetitious DNA)

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

Segment of DNA which can be transcribed and translated to amino acid

 Plant contains about 10 000 – 30 000 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
House keeping gene:
The genes which every cell needs for such basic functions independent of its specialization

Basic functions
+
Microbes highly specialized
Yeast – simplest eukaryote
Fly – complex development
Worm – programmed 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
.

Small difference in gene number, although rice genome is
3x the size

st