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Genomes
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
Genome size
Plant Viruses
Plant DNA viruses are rare
Cauliflower mosaic virus
Spherical, kills Cauliflower and Brussel Sprouts
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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
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Plant Viroids
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
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
Eschericia Coli genome
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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
Agrobacterium tumefaciens
genome
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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)
• T-DNA integrates stably into plant genome
• Single stranded T-DNA fragment is converted to dsDNA
fragment by plant cell
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Then integrated into plant genome
2 x 23bp direct repeats play an important role in the excision
and integration process
Plasmids
Naturally Extra chromosomal circular DNAs
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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
Yeast genome
Genome of diploid Saccharomyce cerevisiae cell
Characteristic
Relative amount (%)
Number of copies
Size (kbp)
Chromosomes
85
2 x 16
14.000
Plasmid
5
60-100
6,318
Mitochondiral
10
~50 (8-130)
70-76
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 regions
• Scarcity of introns
• Lack of repetitive sequences
 Strong evidence of duplication:
• Chromosome segments
• Single genes
 Redundancy: non-essential genes provide selective advantage
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
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
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
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
Genome composition
1. Heterochromatin
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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
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Lightly staining portion of chromosomes
It represents most of the genomes
It contains most of genes.
Ploidy and chromosome number
Organism
Ploidy
Chromosome number
Corn
Diploid (2X)
20
Tomato
Diploid (2X)
24
Arabidopsis
Diploid (2X)
10
Potato
Tetraploid (4X)
48
Wheat
Hexaploid (6X)
42
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
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)
Gene classification
Chromosome
(simplified)
coding genes
Messenger RNA
intergenic
region
non-coding
genes
Structural RNA
Proteins
transfer
RNA
Structural proteins
Enzymes
ribosomal
RNA
other
RNA
Protein Coding Genes
Segment of DNA which can be transcribed and translated to amino acid
Protein Coding 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 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
What do the genes encode?
Microbes
highly
specialized
Basic functions
+
Yeast –
simplest
eukaryote
Fly –
complex
development
Genes for basic cellular functions such as translation,
transcription, replication and repair share similarity
among all organisms
Worm –
programmed
development
Arabidopsis –
plant life cycle
Gene families expand to
meet biological needs.
Plant genome sizes
Predicted Gene numbers
Small difference in gene number, although rice genome is
3x the size
How to study Genome?
Genomics
21st century Biology:
integration