genome sizes and number of genes summary

Gary Williams x3294 gwilliam at crc.ac.uk
Mon Aug 24 11:13:35 EST 1992


The latest values I have for the genome sizes and number of genes
of species in the various genome programs are:

Species        Genome size       No. of genes

E.coli            4.7 Mbp         2,500 to  5,000
Yeast            14   Mbp         8,000
Nematode        100   Mbp        16,000 to 20,000
Drosophila      165   Mbp        15,000 to 25,000
Mouse          3000   Mbp        50,000 - 100,000
Human          3000   Mbp        50,000 - 100,000

Many thanks to all those who replied with data.  (Details below). 

The Yeast value for the number of genes was calculated from Chromosome
III.  (Chromosome III has 182 'genes' and is 315,357 bp long (1/44 th of
the total genome)).

The values for Mouse and Human have not been queried, does everyone
agree with them? Are there any values for Arabidopsis or other plants?

---------------------
> From toms at gov.ncifcrf Tue Aug 18 20:52:45 1992
> Date: Tue, 18 Aug 92 15:47:11 EDT
> From: toms at gov.ncifcrf
> To: gwilliam at uk.ac.crc
> Subject: Re: Genome size and no. of genes
> 
> Gary Williams:
> 
> For E. coli, genome size is 4.7e6; see
> 
> @article{Kohara1987,
> author = "Y. Kohara
>  and K. Akiyama
>  and K. Isono",
> title = "The Physical Map of the Whole {E. coli} Chromosome:
> Application of a New Strategy for Rapid Analysis
> and Sorting of a Large Genomic Library",
> journal = "Cell",
> volume = "50",
> pages = "495-508",
> year = "1987"}
> 
> For my thesis I got a personal communication estimate from someone
> in Neidhart's lab on the number of genes:
> 
> @article{Schneider1986,
> author = "T. D. Schneider
>  and G. D. Stormo
>  and L. Gold
>  and A. Ehrenfeucht",
> title = "Information content of binding sites on nucleotide sequences",
> journal = "J. Mol. Biol.",
> volume = "188",
> pages = "415-431",
> year = "1986"}
> 
> about 2500.
> 
> Also,
> 
> @inproceedings{Fangman1981,
> author = "W. L. Fangman
>  and V. A. Zakian",
> editor = "J. N. Strathern and E.W. Jones and J. R. Broach",
> title = "MISSING",
> booktitle = "The Molecular Biology of the Yeast Sacchromyces",
> publisher = "Cold Spring Harbor Laboratory",
> pages = "28-28",
> comment = "size of yeast genome is 14000 kbp +/- 20%",
> year = "1981"}
> 
> I don't have an estimate of the number of genes, but the recent publication of
> the chromosome III sequence (now available in GenBank I should think) should
> help.
> 
>   Tom Schneider
>   National Cancer Institute
>   Laboratory of Mathematical Biology
>   Frederick, Maryland  21702-1201
>   toms at ncifcrf.gov
>
---------------------
>
> From baillie at ca.sfu Tue Aug 18 04:26:57 1992
> Date: Mon, 17 Aug 92 20:26:44 -0700
> From: baillie at ca.sfu
> To: gwilliam at uk.ac.crc
> Subject: Re: Genome size and no. of genes
> Newsgroups: bionet.molbio.evolution,sci.bio
> Status: RO
> 
> Gary,
> 
> We use the following numbers.
> 
> 1.  essential genes capable of mutation to lethals by knockout
> 	>4000
> 	From our studies on EMS induced lethals in balanced regions
> 	of several chromosomes.
> 2.  detectable conserved elements which have transcripts 
> 	about 3-4 /cosmid in the area around unc-22 on chr IV
> 	nb about 2500 cosmids in genome ----> about 7500 - 10,000 elements
> 3. Sulston, Coulson, Waterston and Wilson Sequencing project, based on the first
> 	megabase of genomic sequence.  About 1 recognizable gene / 4-5 kb
> 	Thus 16-20,000 genes if 80% single copy assumed.
> 
> I would guess that 1/2 to 2/3 of genes are not required under standard 
> 	laboratory growth conditions.
> The essential gene estimates are from a paper      Johnsen and Baillie
> 
> in November Genetics (1991)
> The conserved transcription element estimate from Prasad and Baillie in
> Gemonics 1990.
> 
> And the sequencing data from Sulstton et al. personal communication.
> 
> 
> Please let me know what info you get on the other organisms
> 
> 
> thanks 
> 
> dave baillie
> Institute of Mol. Biol. Biochemistry
> Simon Fraser Univ, Burnaby , BC
> canada
> 
> dbaillie at trog.biol.sfu.ca
> 
---------------------
> 
> From daemon Wed Aug 19 13:29:11 1992
> Date:    Wed, 19 Aug 1992 15:17:40 EDT
> From: LOUIS at gr.uch.cc.talos
> Subject: SUBJECT
> To: gwilliam at uk.ac.crc
> X-Vmsmail-To: in%"gwilliam at crc.ac.uk"
> Status: RO
> 
> X-News: talos bionet.molbio.evolution:270
> 
> 
> As far as Drosophila is concerned, the genome size indicated is clearly wrong.
> The largest genome reported is that of D. virilis (~ 384 Mbp) and the smallest
> (I knoe of) is D. simulans (~120 Mbp).  D. melanogaster, our favorite pet, has
> a genome of ~130-170 Mbp, of which 75% is located in the euchromatic arms of
> the chromosomes.  As to the number of genes, some hard core geneticists say 
> there should be 5000 (meaning mutable loci) and a better number would be 
> 15-25,000 (including all repeats etc.).  I hope other people will give you
> more accurate numbers for the other organisms mentioned.
> kitsos louis
> imbb-forth
> heraklion, crete, greece
> 
---------------------
> 
> From giber at edu.uga.cs.pollux Wed Aug 19 23:18:52 1992
> Date: Wed, 19 Aug 92 18:18:23 EDT
> From: Carolyn Giberson <giber at edu.uga.cs.pollux>
> To: G.Williams at UK.AC.CRC
> Subject: E. coli genes
> 
> Hi Gary,
>    I believe E. coli are estimated to have about 5000 genes.
> 
> Hope this helps!
> Carolyn Giberson
> giber at pollux.cs.uga.edu
> University of Georgia
> 
---------------------
> 
> From MA11 at UK.AC.CAMBRIDGE.PHOENIX Fri Aug 21 12:06:20 1992
> Date: Fri, 21 Aug 92 12:06:04 BST
> From: MA11 at UK.AC.CAMBRIDGE.PHOENIX
> To: g.williams at UK.AC.MRC-CRC
> 
> I saw your bulletin on Bionews. Where did you get the 300MB figure for
> Drosophila from ? The normal figure is given as 165 MB - see Merriam et
> al Science 254:221.
> As for the 15000 figure well it is not an unreasonable guess !
> Michael Ashburner

-- 
GARY WILLIAMS,  Computing Services Section,  Janet:       G.Williams at UK.AC.CRC
MRC-CRC & Human Genome Mapping Centre,       Internet:    G.Williams at CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK
Tel 081-869 3294   Fax 081-423 1275   



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