GenomesGenomes

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 DNA viruses are rareCauliflower mosaic virusSpherical, kills Cauliflower and Brussel Sprouts

Most plant viruses are small and comprised of ssRNA

Rod shaped, attacks tomato, pepper, beets, turnips, tobacco2,130 identical proteins surround the ssRNA~10,000bp, ~10 genes

Plant Viroids

Plant Viruses

Highly complementary circular ssRNANo 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 proteinSome even lack the AUG initiation codon

Replication mechanism is unknownViroids cannot recognize and infect host cell

Relies on cells being weak or injuredProposed that viroids are "escaped introns"

Viroids are usually transmitted by seed or pollenInfected 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

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 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 Agrobacterium tumefaciens genomegenome

• Genome size (chromosome) is about Genome size (chromosome) is about 6 Mb • A large (~250kbp) plasmid called Tumor-inducing (Ti) A large (~250kbp) plasmid called Tumor-inducing (Ti)

plasmid)plasmid)• Plasmid contains genes responsible for the diseasePlasmid contains genes responsible for the disease• Portion of the Ti plasmid is transferred between Portion of the Ti plasmid is transferred between

bacterial cells and plant cells bacterial cells and plant cells T-DNA (Transfer T-DNA (Transfer DNA)DNA)

• T-DNA integrates stably into plant genomeT-DNA integrates stably into plant genome• Single stranded T-DNA fragment is converted to Single stranded T-DNA fragment is converted to

dsDNA fragment by plant celldsDNA fragment by plant cell Then integrated into plant genomeThen integrated into plant genome 2 x 23bp direct repeats play an important role in the 2 x 23bp direct repeats play an important role in the

excision and integration processexcision and integration process

PlasmidsNaturally 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 numbersof 10 - 500 per cells

Genome of diploid Saccharomyce cerevisiae cell

Characteristic Chromosomes Plasmid MitochondiralRelative amount (%) 85 5 10Number of copies 2 x 1660-100 ~50 (8-130)Size (kbp) 14.000 6,318 70-76

Yeast genome

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

RedundancyRedundancy: non-essential genes provide selective : non-essential genes provide selective advantageadvantage

Plant genomes Plant contains three genomesPlant contains three genomes Genetic information is divided in the chromosome.Genetic information is divided in the chromosome. The size of genomes is species dependentThe size of genomes is species dependent The difference in the size of genome is mainly due to a The difference in the size of genome is mainly due to a

different number of identical sequence of various size different number of identical sequence of various size arranged in sequencearranged in sequence

The gene for ribosomal RNAs occur as repetitive The gene for ribosomal RNAs occur as repetitive sequence and together with the genes for some transfer sequence and together with the genes for some transfer RNAs in several thousand of copiesRNAs in several thousand of copies

Structural genes are present in only a few copies, Structural genes are present in only a few copies, sometimes just single copy. Structural genes encoding for sometimes just single copy. Structural genes encoding for structurally and functionally related proteins often form a structurally and functionally related proteins often form a gene familygene family

The DNA in the genome is replicated during the The DNA in the genome is replicated during the interphase of mitosisinterphase of mitosis

Peculiarities of plant genomes Huge genomes reaching tens of billions of base Huge genomes reaching tens of billions of base

pairspairs Numerous polyploid formsNumerous polyploid forms Abundant (up to 99%) non coding DNA which Abundant (up to 99%) non coding DNA which

seriously hinders sequencing, gene mapping and seriously hinders sequencing, gene mapping and design of genedesign of gene

Poor morphological, genetics, and physical Poor morphological, genetics, and physical mapping of chromosomesmapping of chromosomes

A large number of “small-chromosome” in which A large number of “small-chromosome” in which the chromosome length does not exceed 3 the chromosome length does not exceed 3 μμmm

The number of chromosomes and DNA content in The number of chromosomes and DNA content in many species is still unknownmany species is still unknown

Size of the genome in plants and human

GenomeGenome Arabidopsis Arabidopsis thalianathaliana

Zea maysZea mays Vicia fabaVicia faba HumanHuman

NucleusNucleus 70 Millions70 Millions 3900 3900 MillionsMillions

14500 14500 MillionsMillions

2800 2800 MillionsMillions

PlastidPlastid 0.156 0.156 MillionsMillions

0.136 0.136 MillionsMillions

0.120 0.120 MillionsMillions

MitochondMitochondrionrion

0.370 0.370 MillionsMillions

.570 .570 MillionsMillions

.290 .290 MillionsMillions

.017 .017 MillionsMillions

Organisation of the genome into chromosome

The nuclear genome is organized into chromosomeThe nuclear genome is organized into chromosome Chromosomes consist of essentially one long DNA Chromosomes consist of essentially one long DNA

helix wound around nucleosome helix wound around nucleosome At metaphase, when the genome is relatively At metaphase, when the genome is relatively

inactive, the chromosome are most condensed and inactive, the chromosome are most condensed and therefore most easily observed cytologically, therefore most easily observed cytologically, counted or separatedcounted or separated

Chromosomes provide the means by which the Chromosomes provide the means by which the plant genome constituents are replicated and plant genome constituents are replicated and segregated regularly in mitosis and meiosissegregated regularly in mitosis and meiosis

Large genome segments are defined by their Large genome segments are defined by their conserved order of constituent genesconserved order of constituent genes

Genome compositionGenome composition1.1. HeterochromatinHeterochromatin Darkly staining portions of Darkly staining portions of

chromosomes, believed due to high chromosomes, believed due to high degree of coilingdegree of coiling

Non-genic DNANon-genic DNAa. Centromere a. Centromere ~ “middle” of Chromosomes~ “middle” of Chromosomes spindle attachment sitesspindle attachment sitesb. Telomeresb. Telomeres1. ends of chromosome1. ends of chromosome2. important for the stability of 2. important for the stability of chromosomeschromosomes tipstips..

2. Euchromatin2. Euchromatin Lightly staining portion of Lightly staining portion of

chromosomeschromosomes It represents most of the genomesIt represents most of the genomes It contains most of genesIt contains most of genes..

Ploidy and chromosome numberPloidy and chromosome number OrganismOrganism PloidyPloidy Chromosome Chromosome

numbernumberCornCorn Diploid (2X)Diploid (2X) 2020

TomatoTomato Diploid (2X)Diploid (2X) 2424

ArabidopsisArabidopsis Diploid (2X)Diploid (2X) 1010

PotatoPotato Tetraploid (4X)Tetraploid (4X) 4848

WheatWheat Hexaploid (6X)Hexaploid (6X) 4242

Organization of Plant GenomeOrganization of Plant Genome Protein coding geneProtein coding gene

PPortion of genome which encodes for most of the transcribed genes (Protein coding genes)

Non coding gene Non coding gene 1. Intron1. Intron2. 2. Regulatory elements of genes3. Multiple copies of genes, including pseudogenes4. Intergenic sequences5. Interspersed repeats

Organization of Plant GenomeOrganization of Plant GenomeMost plants contain quantities of DNA that greatly

exceed their needs for coding and regulatory functionsVery small percentage of the genome may encode for

genes involved in protein productionBased on kinetics:

Low-copy-number DNALow-copy-number DNADNA 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 DNAHigh-copy-number DNAIIt is composed of highly repetitive sequences (Repetitious DNA)t is composed of highly repetitive sequences (Repetitious DNA)

Gene classificationcoding genes

non-coding genes

Messenger RNA

Proteins

Structural RNA

Structural proteins Enzymes

transfer RNA

ribosomal RNA

otherRNA

Chromosome(simplified)

intergenic region

Protein Coding GenesProtein Coding GenesSegment of DNA which can be transcribed and

translated to amino acid

Protein Coding GenesProtein Coding Genes Plant contains about 10 000 – 30 000 structural genesPlant contains about 10 000 – 30 000 structural genes They are present in only a few copies, sometimes just one They are present in only a few copies, sometimes just one

(single copy gene)(single copy gene) They often form a gene familyThey often form a gene family The transcription of most structural genes is subject to very The transcription of most structural genes is subject to very

complex and specific regulationcomplex and specific regulation The gene for enzymes of metabolism or protein biosynthesis The gene for enzymes of metabolism or protein biosynthesis

which proceed in all cells are transcribed more oftenwhich proceed in all cells are transcribed more often Most of the genes are switched off and are activated only in Most of the genes are switched off and are activated only in

certain organ and then often only in certain cellscertain organ and then often only in certain cells Many genes are only switched on at specific timesMany 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?

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.

Plant genome sizes

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

Predicted Gene numbers

How to study Genome?

Genomics

2121stst century Biology: integration century Biology: integration