Genome Projects

Genome
 Genome
size		 Sequencing Center
(Technology)		 Assembler
 Downloads
 Publication
Sequoia sempervirens
(Coast redwood)		 33 Gbp UC Davis(Illumina)
JHU(ONT)		 MaSuRCA NCBI
CCB		 Project announcement
Sequoia giganteum
(Giant sequoia)		 11 Gbp UC Davis(Illumina)
JHU(ONT)		 MaSuRCA
Dovetail HiRise		 NCBI
CCB		 Project announcement
Pinus taeda
(Loblolly pine)		 22 Gbp UC Davis(Illumina,PacBio) MaSuRCA Treegenesdb
CCB		 Neale et al., Genome Biology 2014
Lomentospora prolificans
(Pathogenic fungus)		 37 Mbp JHU(Illumina)
JHU(ONT)		 megahit
MaSuRCA		 NCBI
CCB		 Salzberg et al., G3 2017
Pinus lambertiana
(Sugar pine)		 31 Gbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 Treegenesdb
CCB		 Stevens et al., Genetics 2016
Pseudotsuga mensiesii
(Douglas fir)		 18 Gbp UC Davis(Illumina) MaSuRCA, SOAPdenovo Treegenesdb
CCB		 Neale et al., G3 2017
Aegilops tauschii
(Goat grass)		 4 Gbp UC Davis(Illumina, BioNano), JHMI(PacBio) MaSuRCA, DeNovoMAGIC NCBI
CCB		 Zimin et al., Genome Research 2017
Luo et al., Nature 2017
Triticum aestivum
(Wheat)		 15 Gbp UC Davis(Illumina,PacBio) MaSuRCA NCBI
CCB		 Zimin et al., GigaScience 2017
Quercus lobata
(Valley oak)		 750 Mbp UC Davis(Illumina,PacBio) MaSuRCA
Dovetail HiRise		 NCBI
CCB		 Sork et al., G3 2016
Juglans regia
(English walnut)		 620 Mbp UC Davis(Illumina), JHU(ONT) MaSuRCA NCBI
CCB		 Martinez-Garcia et al., The Plant Journal, 2016
Juglans microcarpa
(Texas walnut)		 940 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Juglans cathayensis
(Chinese walnut)		 800 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Pterocarya stenoptera
(Chinese wignut)		 950 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Juglans hindsii
(Hind's black walnut)		 650 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Juglans nigra
(Easter black walnut)		 645 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Juglans sigillata
(Iron walnut)		 645 Mbp UC Davis(Illumina) MaSuRCA
SOAPdenovo		 NCBI
CCB		 Stevens et al., G3, 2018
Rhesus macaque
(Macaque)		 2.72 Gbp Baylor College of Medicine HGSC(Sanger,Illumina) MaSuRCA NCBI Zimin et al., Biology Direct 2014
Bombus impatiens
(Common eastern bumble bee)		 250 Mbp University of Illinois (Illumina) SOAPdenovo NCBI
CCB		 Sadd et al., Genome Biology 2015
Megachile rotundata
(Alfalfa leafcutter bee)		 275 Mbp University of Illinois (Illumina) SOAPdenovo NCBI
CCB		 Kapheim et al., Science 2015
Heliconius melpomene
(Tropical butterfly)		 269 Mbp Cornell University (454/Illumina) CABOG NCBI Heliconius Genome Consortium, Nature 2012
Xanthomonas oryzae
(Xanthomonas)		 4.8 Mbp Cornell University (PacBio) HGAP
Celera Assembler, AMOS Minimo		 NCBI Booher et al., Microbial Genomics 2015
Meleagris gallopavo
(Domestic turkey)		 1.2 Gbp Roche/VaTech(454), USDA/NIH(Illumina) MaSuRCA NCBI Dalloul et al., PLoS Biology 2010
Bos taurus
(Domestic cow)		 2.9 Gbp Baylor College of Medicine HGSC (Sanger) Celera Assembler, UMD Overlapper NCBI
CCB		 Zimin et al., Genome Biology 2009
Wolbachia endosymbiont of Culex mosquito(Wolbachia) 1.5 Mbp TIGR, Broad Institute (Sanger) Celera Assembler NCBI Salzberg et al., J. Bacteriology 2009
Francisella tularensis
(Francisella)		 1.9 Mbp Baylor College of Medicine HGSC (Sanger) Celera Assembler NCBI Puiu and Salzberg, PLoS ONE 2008
Pseudomonas aeruginosa Pab1(Pseudomonas) 6.3 Mbp CBCB(Illumina) AMOScmp
Velvet 		NCBI
CCB		 Salzberg et al., PLoS Comp. Biology 2008
Xanthomonas oryzae PXO99A
(Xanthomonas)		 5.2 Mbp TIGR(Sanger) Celera Assembler NCBI
CCB		 Salzberg et al., BMC Genomics 2008
Carica papaya
(Papaya)		 370 Mbp University of Illinois (Sanger) Arachne NCBI Ming et al., Nature 2008
Trichomonas vaginalis 176 Mbp TIGR(Sanger) Celera Assembler NCBI Carlton et al., Science 2007
Brugia malayi 94 Mbp TIGR(Sanger) Celera Assembler NCBI Ghedin et al., Science 2009
Caenorhabditis briggsae
 108 Mbp Sanger Center(Sanger) Celera Assembler NCBI
CCB
 Stein et al., PLoS Biol 2003
Tetrahymena thermophila 103 Mbp TIGR(Sanger) Celera Assembler www.ciliate.org
NCBI		 Eisen et al., PLoS Biol 2006
Trypanosoma cruzi 90 Mbp TIGR(Sanger) Celera Assembler NCBI Najib et al., Science 2005
Drosophila pseudoobscura 164 Mbp Baylor College of Medicine HGSC(Sanger) Celera Assembler CCB
NCBI		 Drosophila 12 Genomes Consortium et al., Nature 2007
Drosophila yakuba 166 Mbp Washington University(Sanger) Celera Assembler NCBI
CCB		 Drosophila 12 Genomes Consortium et al., Nature 2007
Drosophila virilis 206 Mbp Agencourt Bioscience
TIGR(Sanger)		 Celera Assembler NCBI Drosophila 12 Genomes Consortium et al., Nature 2007

GAGE and GAGE-B are evaluations of contiguity and accuracy of assemblies that are generated by some of most commonly used genome assemblers. GAGE-B (for assemblies of bacterial organisms) follows the standards set by GAGE.

Drosophila (fruit fly) endosymbionts

Steven Salzberg and colleagues identified the sequence of the bacterial endosymbiont Wolbachia within the publicly available sequence data of several species of fruit fly. These results were reported in the open access journal Genome Biology:
Salzberg, S.L., Hotopp, J.C., Delcher, A.L., Pop, M., Smith, D.R., Eisen, M.B., Nelson, W.C. (2005) Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol 6 (3):R23.

The assemblies of the endosymbiont genomes were performed with AMOScmp, and they can be obtained from:

Wolbachia endosymbiont of Drosophila annanasae - GenBank entry
Wolbachia endosymbiont of Drosophila simulans - GenBank entry
Wolbachia endosymbiont of Drosophila willistoni - (contigs) (traceIDs)

Older Bacterial Genomes (pre-2006)

Genome
 Genome
size		 Sequencing Center
(Technology)		 Assembler
 Downloads
 Publication
Bacillus Anthracis
Ames Ancestor*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Ravel et al.,
J Bacteriol 2009
Bacillus Anthracis
str. A1055*		 5.4 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Bacillus Anthracis
str. Australia 94*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Bacillus Anthracis
str. CNEVA-9066*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Bacillus Anthracis
str. Kruger B*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Bacillus Anthracis
str. Vollum*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Bacillus Anthracis
str. Western North America USA5153*		 5.5 Mbp TIGR(Sanger) Celera Assembler NCBI
 Rasko DA et al.,
FEMS Microbiology
Review 2005
Borrelia afzelii 1.4 Mbp TIGR(Sanger) Celera Assembler NCBI
 Casjens SR et al..,
J Bacteriol, 2011
Burkholderia cepacia R1808
 8.4 Mbp DOE JGI(Sanger) Celera Assembler NCBI
CCB
Chloroflexus aurantiacus
 5.3 Mbp DOE JGI(Sanger) Celera Assembler NCBI
CCB
Methylobacillus flagellatus
 3 Mbp DOE JGI(Sanger) Celera Assembler NCBI
CCB		 Chistoserdova L et al.,
J Bacteriol, 2007
Xylella fastidiosa ANN1 2.7 Mbp DOE JGI(Sanger) Celera Assembler NCBI
CCB
Xylella fastidiosa DIXON
 2.6 Mbp DOE JGI(Sanger) Celera Assembler NCBI
CCB
*Assemblies completed in partnership with TIGR