Genomes Definition ü ü ü Complete set

Genomes

Definition ü ü ü 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

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

Genome size

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

Plant Viroids Highly complementary circular ss. RNA üNo protein coat üSmaller than viruses (few hundreds of bases) üSmallest known virus is 3. 2 kbp in size üRNA does not code for any known protein üSome even lack the AUG initiation codon ü Replication mechanism is unknown ü Viroids cannot recognize and infect host cell Relies on cells being weak or injured ü Proposed that viroids are "escaped introns" ü Viroids are usually transmitted by seed or pollen ü Infected plants can show distorted growth ü The first viroid to be identified was the Potato spindle tuber viroid (PSTVd) ü Some 33 species have been identified ü

Procaryotic genomes ü ü ü 1. Eschericia coli 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 2. Agrobacterium tumefaciens

Eschericia Coli genome n n 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 118 bp Contour length of genome: 1. 7 mm It can accept foreign DNA derived from any organism

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

Bacterial plasmid

Plasmids üNaturally Extra chromosomal circular DNAs ü ü ü 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

Fungal genomes: S. cerevisiae ü ü ü ü 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

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

Plant genomes ü ü ü ü 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 ü ü ü 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 Zea mays Vicia faba Human Nucleus Arabidopsis thaliana 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 ü ü ü 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. ü ü Heterochromatin Darkly staining portions of chromosomes, believed due to high degree of coiling Non-genic DNA a. Centromere ü ~ “middle” of Chromosomes ü spindle attachment sites b. Telomeres 1. ends of chromosome 2. important for the stability of chromosomes tips. 2. Euchromatin ü ü ü 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 (2 X) 20 Tomato Diploid (2 X) 24 Arabidopsis Diploid (2 X) 10 Potato Tetraploid (4 X) 48 Wheat Hexaploid (6 X) 42

Organization of Plant Genome ü Protein coding gene Portion of genome which encodes for most of the transcribed genes (Protein coding genes) ü 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: ü Low-copy-number DNA sequences encodes for most of the transcribed genes (Protein coding genes) ü Medium-copy-number DNA sequences that encode ribosomal RNA (Tandemly repeated expressed DNA) ü 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 ü ü ü ü 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 3 x the size

How to study Genome? Genomics

21 st century Biology: integration