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GENE AND GENOME OF PLANT
Presented by:
LA ODE B. ABIDIN 10/306997/PMU/6710
SUDARMONO A.T. 11/322094/PMU/6977
Introduction of plant gene and genome
Differences of Nuclear and Organelle genomes
Mechanism involved in dna quantitiy variation
What is GENE?
• Region of DNA or RNA that encode for a polypeptide or for an RNA chain that has a function in the organism
• A modern definition : "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions“
Tree of plant genomes • Nuclear
genome• Mitochondrial
Genomes • Chloroplast
Genomes
What is GENOME?
• GENOME is all of a living thing's genetic material, includes both the genes and the non-coding sequences encoded either in DNA or RNA
Endosymbiotic evolution
Mitochondria arose from α-proteobacteria and chloroplasts arose from cyanobacteria
Nuclear vs Organelle genomes
Nuclear genome structureA chromosome is the visible state of genetic material during a phase of the division of the cell (prometafase/metaphase)
DNA in metaphase chromosomes must be shortened 10,000-fold by very efficient packing.
The DNA molecule is twisted onto itself, and the supercoiled molecule is wrapped around proteins which maintain its shape.
These proteins are histone proteins.
The complex DNA protein is called chromatin, while the structure formed by two turns of DNA around one histone is called a nucleosome.
Chromosome nuclear structure
Overview ofthe many ordersof DNAcondensationinto chromatin
Euchromatine & Heterochromatin• DNA containing genes
is called euchromatin• Non-genic DNA is called
heterochromatin.• Heterochromatin and
euchromatin stain differently.
• This difference causes the bands we see in a karyotype.
Genome composition
• Euchromatin (genes) usually contains a higher proportion of GC.
• Euchromatin has more unique DNA sequences.
• Heterochromatin (non-coding) usually contains a higher proportion of AT.
• Heterochromatin contains more repetitive sequence.s
Differences of organelle and nuclear genomes
No. Differences
Organelle genomes Nuclear genomes
1 DNA Structure Circular DNA Linear DNA2 Packing with histone
proteine No Yes
3 Intron in DNA sequence
No Yes
4 Inheritance Maternal Result of recombination from male and female
5 DNA polymerase DNA polymerase I, low proofreading activity
DNA polymerase 1, 2, 3 and ε with intrinsic proofreading activity
Nuclear genome size in different species
Sizes and coding content of some organelle and prokaryote genomes
Countinued……
Sizes and coding content of some organelle and prokaryote genomes
MECHANISM INVOLVED IN DNA QUANTITIY VARIATION
• Polyploidization• Revetitive
sequence
- rRNA gene
- centromers
- telomeres
- transposons
Ribosomal RNA genes
CENTROMERE
- The telomeres of most organisms' chromosomes consist of short sequence-asymmetric repeated sequences.
- Lengths are typically greater than 50 repeats in holotrichous ciliates, less than 350 repeats in Arabidopsis and 300 to 500 bp in Saccharomyces.
• A Drosophila chromosome, an exception, has a transposable element at the end of one of its chromosomes.
• Examples:
telomere Sentromere Knob
TELOMERES
Transposable Elements (TEs)
50-80% of plant genomes are
TEs
Discovered by Barbara
McClintock by studying unstable
corn kernel phenotypes
Fragments of DNA that can
insert into new chromosomal
locations
Often duplicate themselves
during the process of moving
around
Class 1 TEs use RNA intermediates to move around and undergo duplicative
transposition
Class 2 TEs are excised during transposition and may undergo “cut and paste”
transposition with no duplication or “gap repair” where the gap is filled with a
copy of the transposon
Autonomous elements contain necessary genes for transposition
Non-autonomous elements rely on products of other elements for transposition
• Move by a "cut andpaste" process: thetransposon is cut out ofits location andinserted into a newlocation• Requires atransposase to cut andinsert DNA fragment.• Transposon hasterminal invertedrepeats• Excision generatesdirect repeats (~ targetinsertion sites)
Class II Transposons
CONCLUSION
- The genomes are very dynamic- Genome of plant is located in
nuclues, mitochondria and chloroplast
- Genetic element is changed at different scales:• Gene• Chromosome segments• Genome
Literature1. Jenik, P.D. Jurkuta, R.E. and Barton, M.K. 2005.
Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon. Plant Cell 17: 3362–3377
2. Parent, J. Lepage, E. and Brisson, N. 2011. Divergent Roles for the Two PolI-Like Organelle DNA Polymerases of Arabidopsis. Plant Physiology 156 (1): 254-262
3. Pearson, H. 2006. Genetics: what is a gene?. Nature 441: 398-401
4. Quiroz, H.C.2002. Plant genomics: an overview. Biological Research 35: 3-4
5. Ridley, M. 2006. Genome. New York, NY: Harper Perennial.
6. Timmis, J.T. Ayliffe, M.A. Huang, C.Y. and Martin, W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nature 5: 123-135.
7. Casacuberta and Santiago, 2003, Plant LTR-retransposons and MITEs: control of transcription and impact on the evolution of plants genes and genomes. Elsevier Gene 311 (2003) 1-11.
Terima kasih…..
Coordination between the nucleus and organelle genomes
Anterogade signaling
Anterogade signaling
Retrogade signaling
Retrogade signaling
Polyploidy (here, autopolyploidy)
Structure of the different types of plant transposable elements