Deoxy Ribonucleic Acid

Deoxy Ribonucleic Acid

Introduction:

DNA molecules are made up of a string of deoxy ribonucleotides held by phosphodiester bonds. These molecules are made on polynucleotide templates; so also, RNA molecules. Quantity of DNA per cell for a given organism is constant and proportional to the ploidy i.e. per set of chromosomes, which varies from one organism to another organism. Lower organisms such as bacteria and viruses don’t have chromosomes and their genomic DNA is suspended in the cell or enclosed in a capsid (virus). The size of the genome in plants and animals vary by several folds, which is why it is called C-DNA (haploid DNA) value paradox. Ex. Humans contain 3.2x10^9bp genome but Paris (Pieris) japonica contains 52.3 times that of human genome. 1pg = 978x10^6bp = 0.978 x 10^9bp

Genome sizes:

Prokaryotic Organisms (some):

Name of the species	Genome size	Number of Genes	Size of Genes
Mycoplasma genitalium,G37	0.582 x 10 ⁶bps	521 (protein 475 genes)	1040 bp
Mycoplasma pneumoniae	1 x 10 ^{6 bps}
Myxophyceae: Dictyostelium discoideum	5.4 x 10 ⁷bp

Bacteria:

Name	Size of the Genome	Number of Genes	Size of genes
Synochocystis(cytobacteria)	3.7 x 10^{6 bp}
Rikettsia prowazeskii	1.1 x 10^6 bp	834
Homophilus influenzae	1.83x10^6bp	1.83x10^6
E.coli k12	4, 641,652bp	4141+176	1072

Eukaryotic organisms: Chromosome Numbers:

Some Plants (haploid numbers):

Species	N=?
Saccharomyces	16
Neurospora crassa	7
Aspergillus nidulens	8
Penicillium species	4
Dictyostelium discoideum	7
Chlamydomonas reinhardii	16
Acetabularia	10
Antirrhinum majus (snap dragon)	8
Lycopersicon esculentum	12
Nicotiana tabaccum	24
Pinus sylvestris	12
Phaseolus vulgaris (French bean)	7
Pisum sativum	7
Vicia faba	6
Allium cepa	8
Allium sativum	?
Hordeum vulgare (barley)	7
Triticum monococcum (wheat)	12
Zea mays	10

Some Animals (haploid numbers):

Species	Chromosome number, n=?
Hydra	16
Planaria torva	8
C. rhabditids’	2n=11 male 2n=12 female
Musa domestica	6?
Drosophila melanogaster	4
Bombax mori	28?
Rana pipens	13
X laevis	13?
Gallus domesticus (chick)	39
Felis domesticus (cat)	19
Cannis familiaris (dog)	39
Bos taurus (cattle)	30
Equs calibus (horse)	32
Mus musculus (mice0	20
Rattus norvigicus	22
Mesocricetus auratus (golden hamster0	22
Cavia cobaya (guinea pig)	32
Oryctolagus cuniculus (rabbit)	22
Macaca mulitas (Rhesus monkey)	21
Orangutan	24
Gorilla gorilla	24
Homo sapiens	23

Genome size:

Few Plants:

Few Animals:

Species		Genome size	Gene Numbers
Pyrenoma salina (an algae)		6.6 x 10^5 bp
Neurospora crassa.		2.7 x 10^7bp
Saccharomyces cerevisiae, n=16		1.35 x 10^7 bp	~6034
Chloro arachnophile, an algae, and a nucleomorph (lives in a nucleus)		3.8 x 10^5 bp
Cryptophyte, a nucleomorph, n=3		6 x 10^5 bp
Nicotiana tabaccum		4.8 x 10^9 bp
Prunus parsica		2.62 x 10^8 bp
Ricinus communis		3.23 x 10^8 bp
Citrus sienensis		3.67 x 10^8 bp?
Petunia paradii		1.221 x 10^9 bp
Pisum sativum, n=7		1.1315 x 10^9 bp
Arabidopsis thaliana		1.5 x 10^8 bp	10000 (proteins=10^5)
Zea mays		5 x 10^9 bp	20000 (Proteins=4x10^6). 250000
Oriza sativa		4.66X 10^8	40 000
Avena sativa		1.315 x 10^10 bp
Tulipa		2.47 x 10^10 bp
Lillium formosanum-Lily		3.6 x 10^10 bp	15000
Ophioglossum petiolatum		1.6x10^12	20000
Allium cepa		1.8x10^9	20000
Psilotum nudum
Fritillaria assyrica	130x10^9bp=132pg
Paris japonica	150x10^9bp=152g

Few Animals:

Species	Genome size
Plasmodium falciparum	2.7 x 10^7 bp
C.elegans (a nematode), n=6	8 x 10^7 bp
D.melanogaster, n=4	1.4-1.65 x 10^8 bp
House fly, n=4	8.6 x 10^8 bp
Pond frog	2.3 x 10^10 bp
X.laevis, n=13?	3.1 x 10^9 bp
Sea urchin	8.0 x 10^8 bp
Zebra fish; Danio revio	1.7 x 10^7 bp
Lung fish, n=19	1.02 x 10^11 bp
Gallus domesticus (chick), n=	1.2 x 10^9 bp
Mus musculus (mice)	2.6 x 10^9 bp
Rattus norvigeticus (rat)	3 x 10^9 bp
Homosapiens, n=23	2.9 x 10^9 bp in males? 3.3 x 10^9 bp in females?
Polychaos dubium	670X10^9bp, 670GB
Protopterus aethiopicus	130x10^9= 130Gb

Organelle DNA:

Chloroplasts: Plastome:

Species	Genome size	Genome number per organelle	Organelle per cell
Chlamydomonas	180kbp, circular, codes for 120 to 150 proteins	80	One
Maize= Zea mays; nucleoids	120-200kbp, circular, codes for 120 to 150 proteins	20-40	20-40
Liverwort (Bryophyte)	121kbp, circular
Nicotiana tabacum	155,939bp, circular
Arabidopsis thaliana	154,478Bp
Cocos nucifera	154,731Bp
Vigna radiata	151,271Bp
Welwitschia	120-160,000Bp
Phuyllostachys edulis(woody bamboo)	139,679bp

Mitochondria:

Species		Genome size, number of proteins produced	Genome numbers per organelle	Number of organelle per cell
Homo sapiens		16.569bp, circular, codes for 13 proteins, 5-7 URFs, no introns	5-10	200-1000 or more
S. cerevisiae		84kbp, contain introns, codes for 13 proteins, few URFs, contain introns	20-50	1-200
Frog’s Oocyte			5-10	10^6 to 7
Neurospora		19-108kbp, contain introns	10-20	50-100
Chlamydomonas		16000, linear	5-10	1?
Species		Master Circle Size (kb)	Sub-genomic Circle Size (kb)	Repeat Size (kb)
Turnip		218	135 + 83	2
Cauliflower		217	172 + 45	?
Black Mustard		231	135 + 96	7
White Mustard		208	none	none
Radish		242	139 + 103	10

Rice	-490,520kBp
Arabidopsis thaliana-	366,974 (57genes),
Wheat-	105-704kbp
Cucumber	~200kbp
Hu-	16,9569, bp,
Melon,	-2.4mbps
Maize-	569630bp,
C.elegans-	13,794 bps,
S.cerevisiae Yeast-	85.779KBp
Corn-	570KBp
Turnip-	218KBp
Oenothers-	195KBP
Muskmelon-	2400 kbp

Some of the Genomic work completed:

E. coli: 1991-1997; n = 1; = 4.6x10^6; no. of genes = 4405; genes similar to humans are not known.

Yeast: 1989-1996; n=16 = 1.2 x10^7 bp; number of genes = 6241; there are 120 out of human’s 289 genes on mutations to cause disease. Information indicates that its mechanisms are as complex as any other organism.

C.elegans:1990-98; n = 6 = 1x10^8bp; no. of genes = 19000; 9500 genes are approximately similar to Human genes. This is an excellent system to understand cell lineage and tissue construction.

Fruit fly: 1999-2000; n = 4; = 1.8x10^8;bp, no. of genes = 13000; among them 177 genes are similar to humans.

Arabidopsis thaliana: 1996-2000; n= 5; = 1.18x^8; no. of genes = 25500, about 100 genes are similar to that of Humans.

Pieris japonica- 152pg = 978x10^6bp,

Frittilaria aethiopicus- 132.5pg,

Polychoas dubia - 670 x 10^9bp.

Mouse: Gallus gallus; 1999-2005; n = 40? Number of genes = 40000; a majority of them are related to or similar humans.

Human: 1990-2003; n = 23; 3pg = 3.3x10^9; estimated number of gene varies, theoretically 150, 000, but actually the number is about 21-22 000.

Interesting genomic sizes:

Candidatus Carsonella ruddii: 160kb

Encephalitozoon intestinalis: 0.0023pg human intestine parasite (smallest genome).

Fritillaria assyriaca: (Trillium × Hagee), Fritillary (132.50 pg).

Proteopterus aethiopicus: marbled lung fish with 132.83 pg.

Paris japonica: 152.3 pg; = 152.3 x 978 x 10^6 bp; Number of genes? ~148.9 x 10^9bp (1pg = 0.978 x10^6)

Polychaos dubium: 670 x 10^9 base pairs; an amoeba-largest genome.

Organisms used and time taken for size/sequence analysis:

Organism	#bp	Time in hrs/days	#genes	#bp/gene
PhiX174	5386 bp	1.5hrs	9	598
E. coli	4639 221 bp	54 days	4288	1072
S. cerevisiae	12 057849bp	140	6269	1923
C.elegans	~97000000bp	3.1yrs	19099	5079
A. thaliana	~125000 000bp	4yrs	25498	4902
D.melanogastor	~180 000 00bp	5.7yrs	13600	13235
H. sapiens	~3.2 x 10^9bp	108yrs	22000	113 333
Pieris (Paris) japonica	~3.2x15x10^9			15 times human genome

Genome Sizes:

The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of environmental conditions). In this sense, then, diploid organisms (like us) contain two genomes, one inherited from mother, the other from father. In flowering plants, it can be bisexually or unisexually inherited.

The majority of modern genome size estimates is based on either Feulgen densitometry (more recently using computerized image analysis) or flow cytometry, although DNA reassociation kinetics, bulk fluorometry, static fluorometry, DAPI method, Propidium iodide, Electrophoretic methods, Quantitative real-time PCR and complete genome sequencing have also been used.

Genome sizes are typically given as gametic nuclear DNA contents (‘C-values’) either in units of mass (picograms, where 1 pg = 10⁻¹² g) or in number of base pairs (in eukaryotes, most often in mega bases, where 1 Mb = 10⁶ bases). These are directly interconvertible as 1 pg = 978 Mb (or 1 Mb = 1.022 × 10⁻³ pg). Note: 1pg of ds DNA= 0.978 x 10^9 bp. The term "C-value enigma" represents an update of the more common but outdated term "C-value paradox. "C-value" (Swift 1950) refers to haploid nuclear DNA content. The term was coined by Canadian biologist Dr. T. Ryan Gregory of the University of Guelph in 2000/2001.

Tree of life with genome sizes as outer bars; http://www.en.wikipedia.org

The table below presents a selection of representative genome sizes from the rapidly-growing list of organisms whose genomes have been sequenced.

Comparison of different genome sizes(Wikipedia)

http://en.wikipedia.org/

Table of Genome Sizes (haploid)
	Base pairs	Genes	Notes
φX174	5,386	11	virus of E. coli
Human mitochondrion	16,569	37
Epstein-Barr virus (EBV)	172,282	80	causes mononucleosis
Nanoarchaeum equitans	490,885	552	This parasitic member of the Archaea has the smallest genome of a true organism yet found.
Nucleomorph of Gaillardia theta	551,264	511	all that remains of the nuclear genome of a red alga (a eukaryote) engulfed long ago by another eukaryote
Mycoplasma genitalium	580,073	485	two of the smallest true organisms
Mycoplasma pneumoniae	816,394	680	two of the smallest true organisms
Chlamydia trachomatis	1,042,519	936	this bacterium causes the most common sexually-transmitted disease (STD) in the U.S.
Rickettsia prowazekii	1,111,523	834	bacterium that causes epidemic typhus
Treponema pallidum	1,138,011	1,039	bacterium that causes syphilis
Mimivirus	1,181,404	1,262	A virus (of an amoeba) with a genome larger than the six cellular organisms above
Pelagibacter ubique	1,308,759	1,354	smallest genome yet found in a free-living organism (marine α-proteobacterium)
Borrelia burgdorferi	1.44 x 10⁶	1,738	bacterium that causes Lyme disease [Note]
Campylobacter jejuni	1,641,481	1,708	frequent cause of food poisoning
Helicobacter pylori	1,667,867	1,589	chief cause of stomach ulcers (not stress and diet)
Thermoplasma acidophilum	1,564,905	1,509	These unicellular microbes look like typical bacteria but their genes are so different from those of either bacteria or eukaryotes that they are classified in a third kingdom: Archaea.
Methanococcus jannaschii	1,664,970	1,783
Aeropyrum pernix	1,669,695	1,885
Methanobacterium thermoautotrophicum	1,751,377	2,008
Hemophilus influenzae	1,830,138	1,738	bacterium that causes middle ear infections
Streptococcus pneumoniae	2,160,837	2,236	the pneumococcus
Neisseria meningitidis	2,184,406	2,185	Group A; causes occasional epidemics of meningitis in less developed countries.
Neisseria meningitidis	2,272,351	2,221	Group B; the most frequent cause of meningitis in the U.S.
Encephalitozoon cuniculi	2,507,519	1,997	(plus 69 RNA genes); a parasitic eukaryote.
Propionibacterium acnes	2,560,265	2,333	causes acne
Listeria monocytogenes	2,944,528	2,926	2,853 of these encode proteins; the rest RNAs
Deinococcus radiodurans	3,284,156	3,187	on 2 chromosomes and 2 plasmids; bacterium noted for its resistance to radiation damage
Synechocystis	3,573,470	4,003	a marine cyanobacterium ("blue-green alga")
Vibrio cholerae	4,033,460	3,890	in 2 chromosomes; causes cholera
Mycobacterium tuberculosis	4,411,532	3,959	causes tuberculosis
Mycobacterium leprae	3,268,203	1,604	causes leprosy
Bacillus subtilis	4,214,814	4,779	another bacterium
E. coli K-12	4,639,221	4,377	4,290 of these genes encode proteins; the rest RNAs
E. coli O157:H7	5.44 x 10⁶	5,416	strain that is pathogenic for humans; has 1,346 genes not found in E. coli K-12
Agrobacterium tumefaciens	4,674,062	5,419	Useful vector for making transgenic plants; shares many genes with Sinorhizobium meliloti
Salmonella enterica var Typhi	4,809,037	4,395	+ 2 plasmids with 372 active genes; causes typhoid fever
Salmonella enterica var Typhimurium	4,857,432	4,450	+ 1 plasmid with 102 active genes
Yersinia pestis	4,826,100	4,052	on 1 chromosome + 3 plasmids; causes plague
Schizosaccharomyces pombe	12,462,637	4,929	Fission yeast. A eukaryote with fewer genes than the four bacteria below.
Ralston solanacearum	5,810,922	5,129	soil bacterium pathogenic for many plants; 1681 of its genes on a huge plasmid
Pseudomonas aeruginosa	6.3 x 10⁶	5,570	Increasingly common cause of opportunistic infections in humans.
Streptomyces coelicolor	6,667,507	7,842	An actinomycete whose relatives provide us with many antibiotics
Sino rhizobium melilotus	6,691,694	6,204	The rhizobial symbiont of alfalfa. Genome consists of one chromosome and 2 large plasmids.
Saccharomyces cerevisiae	12,495,682	5,770	Budding yeast. A eukaryote.
Cyanidioschyzon Merola	16,520,305	5,331	A unicellular red alga.
Plasmodium falciparum	22,853,764	5,268	Plus 53 RNA genes. Causes the most dangerous form of malaria.
Thalassiosira pseudonana	34.5 x 10⁶	11,242	A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteins
Neurospora crassa	38,639,769	10,082	Plus 498 RNA genes.
Naegleria gruberi	41 x 10⁶	15,727	This free-living unicellular organism lives as both an amoeboid and a flagellated form. 4,133 of its genes are also found in other eukaryotes suggesting that they were present in the common ancestor of all eukaryotes. The great variety of functions encoded by these genes also suggests that the common ancestor of all eukaryotes was itself as complex as many of the present-day unicellular members.
Caenorhabditis elegans	100,258,171	21,733	The first metazoan to be sequenced.
Arabidopsis thaliana	115,409,949	~28,000	a flowering plant (angiosperm) See note.
Drosophila melanogaster	122,653,977	~17,000	the "fruit fly"
Anopheles gambiae	278,244,063	13,683	Mosquito vector of malaria.
Tetraodon nigroviridis (a pufferfish)	3.42 x 10⁸	27,918	Although Tetraodon seems to have more protein-encoding genes than we do, it has much less "junk" DNA so its total genome is about a tenth the size of ours.
Rice	3.9 x 10⁸	28,236
Sea urchin	8.14 x 10⁸	~23,300
Zebrafish	1.2 x 10⁹	15,761
Dogs	2.4 x 10⁹	19,300
Humans	3.3 x 10⁹	~21,000	[Link to more details.]
Mouse	3.4 x 10⁹	~23,000
Amphibians	10⁹–10¹¹	?
Psilotum nudum	2.5 x 10¹¹	?	Note, 3000 times the genome of A. thaliana
Porcine circovirus type1	1,759bp

Note: The DNA from a single (diploid) human cell, if the 46 chromosomes were connected end-to-end and straightened, would have a length of ~2 m and a width of ~2.4 nanometers

Origin of the term Genome:

The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg (Germany). In Greek, the word genome (γίνομαι) means "I become, I am born, I come into being". The Oxford English Dictionary suggests the name to be a blend of the words, gene and chromosome. A few related -ome words already existed, such as proteome, transcriptome, biome and rhizome, forming a vocabulary into which genome fits systematically.

GENOME: Refer to ENCODE: Encyclopedia Of human DNA Elements

An analogy to the human genome stored on DNA is that of instructions stored in a book:

· The book (genome) would contain 23 chapters (chromosomes);

Each chapter contains 48 to 250 million letters (A, C, G, T) without spaces;

· Hence, the book contains over 3.2 billion letters total;

· The book fits into a cell nucleus the size of a pinpoint;

· At least one copy of the book (all 23 chapters =23) is found in most of the cells in our body. The only exception in humans is found in mature red blood cells which become enucleated during development and therefore lack a genome. www.wikipedia