Genome projects

Our group has been assembling genomes for many years, ranging from tiny (viruses and bacteria) to enormous (pine trees). We also develop genome assembly algorithms and software. This continues to be a very active area for the lab. Here we list some of the genomes that we’ve assembled along with the publications. All data has been (or will be) deposited in GenBank.

Species Common name Genome size Publication
Sequoia sempervirens Coast redwood 33 Gbp Project announcement here
Sequoia giganteum Giant sequoia 11 Gbp Project announcement here
Pinus taeda Loblolly pine 22 Gbp Neale et al., Genome Biology 2014
Lomentospora prolificans Pathogenic fungus 37 Mbp Salzberg et al., G3 2017
Pinus lambertiana Sugar pine 31 Gbp Stevens et al., Genetics 2016
Pseudotsuga mensiesii Douglas fir 18 Gbp Neale et al., G3 2017
Aegilops tauschii Goat grass 22 Gbp Zimin et al., Genome Research 2017
Triticum aestivum Wheat 15 Gbp TBA
Quercus lobata Valley oak 750 Mbp Sork et al., G3 2016
Juglans regia English walnut 620 Mbp Martinez-Garcia et al., The Plant Journal, 2016
Juglans microcarpa Texas walnut 940 Mbp TBA
Juglans cathayensis Chinese walnut 800 Mbp TBA
Pterocarya stenoptera Chinese wingnut 950 Mbp TBA
Juglans hindsii Hind’s black walnut 650 Mbp TBA
Rhesus macaque Macaque 2.72 Gbp Zimin et al., Biology Direct 2014
Bombus impatiens Common eastern bumble bee 250 Mbp Sadd et al., Genome Biology 2015
Megachile rotundata Alfalfa leafcutter bee 275 Mbp Kapheim et al., Science 2015
Heliconius melpomene Tropical butterfly 269 Mbp Heliconius Genome Consortium, Nature 2012
Xanthomonas oryzae Xanthomonas 4.8 Mbp Booher et al., Microbial Genomics 2015
Meleagris gallopavo Domestic turkey 1.2 Gbp Dalloul et al., PLoS Biology 2010
Bos taurus Domestic cow 2.9 Gbp Zimin et al., Genome Biology 2009
Wolbachia endosymbiont of Culex mosquito Wolbachia 1.5 Mbp Salzberg et al., J. Bacteriology 2009
Francisella tularensis Francisella 1.9 Mbp Puiu and Salzberg, PLoS ONE 2008
Pseudomonas aeruginosa Pab1 Pseudomonas 6.3 Mbp Salzberg et al., PLoS Comp. Biology 2008
Xanthomonas oryzae PXO99A Xanthomonas 5.2 Mbp Salzberg et al., BMC Genomics 2008
Carica papaya Papaya 370 Mbp Ming et al., Nature 2008

Virtually all of the projects listed here are collaborations with other labs; see the publications for a list of all the scientists involved on each one. Many older genomes are not listed here, including dozens of bacterial genomes sequenced when the lab was at TIGR (1997-2005) and the University of Maryland (2005-11), and hundreds of influenza virus genomes sequenced at TIGR for the Influenza Genome Sequencing Project, which our lab co-founded and which is still ongoing at NIAID.