Numbers of putatively functional full-length CYP genes in 54 whole eukaryotic genomes

August 9, 2004 D. Nelson

Vertebrates (deuterostomes)

Homo sapiens (human)                                               57                    Apr. 2003

Pan troglodytes (chimp)                                              ? (probably 57 or 58)

Mus musculus (mouse)                                               102                  Feb. 2003 build 30

Rattus norvegicus (rat)                                                ?

Canis familiaris (dog)                                                 54                   Sep. 2003

Bos taurus (cow)                                                         at least 53

Gallus gallus (chicken)                                               at least 41

Takifugu rubripes (pufferfish)                                    54                    Aug. 2002 v.3.0

Tetraodon nigroviridis (freshwater puffer)                 ?

Danio rerio (zebrafish)                                               at least 81

Urochordates (deuterostomes)

Ciona intestinalis (sea squirt)                                      80                   Dec. 2002

Ciona savignyi (sea squirt)                                          97                   Apr. 2003 release 1

Echinoderms (deuterostomes)

Strongylocentrotus purpuratus (purple sea urchin)     ?

Genome size = 870Mb, based on haploid genome of 0.89pg X 0.978 pg/Gb

White paper states genome size is about 800Mb.

At Caltech:

Database: purpuratus-complete

Posted date:  June 11, 2004

Number of letters in database: 67,056,103 about 8%

Number of sequences in database:   89,094

Database:  BAC-end sequence tag connectors (STCs)

Number of letters in database: 46,412,324 about 5% of the genome

Number of sequences in database:  76,020

Database: purpuratus-pmc-ests (ESTs of primary mesenchyme cells)

10,206 sequences; 7,908,988 total letters

 

at Baylor: (BLASTN only)

Posted date:  Sep 25, 2003

Spurpuratus/genome/Spur20030922-genome

90,680 sequences; 269,576,112 total letters, about 30% of genome

at NCBI:

over 8.1 million traces in shotgun and WGS (at about 500bp/read)

This may be about 4Gb or about 4-5X coverage

Insects (protostomes)

Drosophila melanogaster (fruit fly)                           84                    Mar. 2000

Drosophila pseudoobscura (a second fly)                  79

Drosophila simulans http://www.genome.wustl.edu/blast/client.pl

# of letters in database:  155,439,225

# of sequences in database:  98,443

 

Drosophila yakuba http://www.genome.wustl.edu/blast/client.pl

# of letters in database:  169,400,961

# of sequences in database:  23,959

 

Anopheles gambiae (mosquito)                                   105                  Oct. 2002

Bombyx mori (silkworm)                                            ~79

 

Apis mellifera (honeybee)                                           ~60

 

Nematodes (protostomes)

Caenorhabditis elegans (nematode)                            74                    Dec. 1998

Caenorhabditis briggsae (a second nematode)           ?

 

Mycetozoa

 

Dictyostelium discoideum (slime mold)                      42                   Apr. 2003

Plants

Arabidopsis thaliana (thale cress)                               249                  Dec. 2000

Oryza sativa (rice)                                                      323                  Apr. 2002

Chlamydomonas reinhardtii (green algae)                  at least 33

Cyanidioschyzon merolae (red algae)                         5

Fungi

Neurospora crassa (bread mold)                                38                   Apr. 2003

Saccharomyces cerevisiae (bakerŐs yeast)                    3                    Oct. 1996

Schizosaccharomyces pombe (fission yeast)                2                    Feb. 2002

Fusarium graminearum (plant pathogen, fungi)         110

 

Magnaporthe grisea (rice blast fungus)                      120

 

Aspergillus nidulans (plant pathogen, fungi)               111

 

Aspergillus fumigatus (filamentous fungi)                  ?

 

Candida albicans                                                        ?

http://sequence-www.stanford.edu/group/candida/index.html

 

Coprinus cinereus 10X coverage

http://www.broad.mit.edu/annotation/fungi/coprinus_cinereus/whatsnew.html

 

Ustilago maydis 10X coverage

http://www.broad.mit.edu/annotation/fungi/ustilago_maydis/whatsnew.html

 

Cryptococcus neoformans 11X coverage 24Mb

http://www.broad.mit.edu/annotation/fungi/cryptococcus_neoformans/index.html

 

Encephalitozoon cuniculi                                            0

 

Botrytis cinerea = Botryotinia fuckeliana (fungi) 5X  ?

sequenced at Syngenta (private), cDNA project at Genoscope

Natalie L. Catlett, Olen C. Yoder, and B. Gillian Turgeon*

Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens

Eukaryotic Cell, December 2003, p. 1151-1161, Vol. 2, No. 6

Torrey Mesa Research Institute/Syngenta Research and Technology, San Diego, California 92121

 

Gibberella moniliformis = Fusarium verticillioides   5X        ?

sequenced at Syngenta (private)

Natalie L. Catlett, Olen C. Yoder, and B. Gillian Turgeon*

Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens

Eukaryotic Cell, December 2003, p. 1151-1161, Vol. 2, No. 6

Torrey Mesa Research Institute/Syngenta Research and Technology, San Diego, California 92121

 

Cochliobolus heterostrophus = Bipolaris maydis 5X             ?

sequenced at Syngenta (private)

Natalie L. Catlett, Olen C. Yoder, and B. Gillian Turgeon*

Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens

Eukaryotic Cell, December 2003, p. 1151-1161, Vol. 2, No. 6

Torrey Mesa Research Institute/Syngenta Research and Technology, San Diego, California 92121

 

Alveolates/Ciliates (free living)

 

Tetrahymena thermophila (ciliate)                              48

 

Paramecium tetrauralia (ciliate)                                 22

 

Alveolates/Apicomplexan parasites

 

Plasmodium falciparum (malaria)                               0

 

Stramenopiles, heterokonts, Chromista

 

Phytophthora ramorum (Sudden Oak Death)            24

 

Phytophthora sojae (stramenopile)                             29

 

Thalassiosira pseudonana (centric marine diatom)    10

 

Euglenozoans

 

Trypanosoma cruzi (Chagas disease, euglenozoan)    3

 

Trypanosoma brucei (African sleeping sickness)       2

 

Trypanosoma vivax (euglenozoan)                             2

 

Trypanosoma congolense (euglenozoan)                    2

 

Leishmania major (Leishmaniasis organism, euglenozoan)    4

 

Leishmania infantum (euglenozoan)                           4

 

Parabasala, Archaezoa

 

Giardia lamblia (hiker's diarrhea)                               0