I.  Large size of plant Genomes
		E. coli 		4.5 kB
		yeast  		1.2 x 104 kB
		C. elegans 	9.7 x 104 kB
		Arabidopsis	1.3x 10 5 kB
		Drosophila 	1.8 x 10 5 kB
		Mung bean	3 x 105 kB
		Human 		3.2 x106 kB
		Pea 		4.5 x 106 kB
		Maize		2.5 x10 6 kB
		Broad bean	13x 10 6 kB
		Wheat 		16x 106 kB

		Genomics indicate a near constant number of genes (26,000 in arabidopsis, 30-40,000 in 				humans, 19,099 in C. elegans, 13,600 in drosophila)
II. Forces in expansion		
	A. Repetitive DNA		
		1. Types
			a. Frequency
				-highly repetitive (105 to 107 per genome) 
				-moderately repetitive (103 to 105 per genome)
				- unique sequences 1-3 per genome
			b. Dispersion
				-tandem repeats- clusters	
                                   functional 
                                      rDNA 18S-5.8S-25S and 5S clusters 
                                      telomeres telomere- repeat  Arabidopsis: (CCCTAAA)n   2-3 kB long
				-dispersed repeats	
					e.g. type I and type II transposable elements
		2. Arabidopsis Repetitive DNA: 
                        a) 10% highly repetitive
				1. 180 bp tandem repeat  4,000-6000 copies centromer repeat
				2. 160 bp tandem repeat	1,500 copies - centromere region
				3. 500 bp tandem repeats 	500-600 copies
				4. 7 bp tandem CCCTAAA 350 copies, at telomere
			b) 10% moderately repetitive
				1. most are rDNA 10Kb segments with 570 copies
				     -18S-5.8S-25S in clusters near telomers on Chrom 2 and 4
				    - 5S near centromeres
				2. transposons 10% of genome (20% of intergenic DNA)
					2,203 Class II transposons
					2,109 Retrotransposons- mostly around centromeres
		3.  Larger genomes have more repetitive DNA
			Arabidopsis 1 x 105 kB		14% repetitive
			Tomato		1x 106 kB	15-20%
			Mung bean	4.5 x 108 kB	30%
			Pea		4.5 x109kB	70%
			Wheat, Corn	1010 Kb		60-80%
				generally more retrotransposons in larger genomes

		         Repetitive DNA stuffs between genes
			Retroelements show some conservation between species 
			Extension of spacer regions with repetitive DNA- e.g. Adh1 gene in Maize vs Sorghum

	B. Duplication of DNA
         	   Forces:
		1. Polyploidy-greater than 2N chromosomes
			- estimate 47-70% of species are polyploid
			a. autopolyploidy: multiplication of chromosomes in one species
			b. allopolyploidy: hybridization of two species genomes
                         -usually sterile since odd number of truly homologous chromosomes; 
                         -nondisjunction produces 4N, fertile
					e.g. bread wheat 42 chromosomes   AABBDD

                 2. Segmental duplication
                      -transposons allow homologous recombination to produce exchange of
                           chromosomal segments, produces duplication of segments
	    Results
		1. Cryptic polyploidy		
			Maize-blocks can also be reassembled into two maize genomes
			Arabidopsis- low duplication- but  only 35% of genes are unique
			     -58% of genes in segmental duplication- 24 duplicated segments 100Kb or 
					longer
			     - 17% of genes as tandem duplication up to 23 copies
			    - evidence of segmental duplication of varying size rather than old tetraploid
                        Soybean-segmental duplication- duplicated sequences  10-42 kb long,
                                 embedded in sea of unduplicated sequences	
                2. Synteny- colinearity of sequence segments- Lego model :  Grasses
                3. Advantages of gene duplication:
	             a. increased expression- histones
	             b. divergence of functions- enzymatic activity 
                     c. divergence of regulatory functions- Chalchone synthase gene- 
                                      defense,UV light, anthocyanins
                     d. higher fidelity- e.g. cyclins
	             e. recombination of functional domains with other domains to combine function
	

Links:
Nucleosomes/chromatin packaging
Database of Genome Sizes
Plant Genome organization-PLSC731 NDSU
Article on grass genome organization-Proceedings National Academy of Sciences 1998, talks about LEGO model
Another article on grass genome organization-Proceedings National Academy of Sciences, 1998, talks about comparisons in genome segments
Microarray technology
Arabidopsis genome summary Aug 1998 - neat poster format!

Nature Genome website

Papers:

The Arabidopsis Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana  Nature 408, 796 - 815  Downloadable supplements in a .zip file

Steven Henikoff, * Elizabeth A. Greene, Shmuel Pietrokovski, Peer Bork, Teresa K. Attwood, Leroy Hood 1997 Gene Families: The Taxonomy of Protein Paralogs and Chimeras  Science 278, pp. 609-614.

Last revised: April 11, 2001- Straney