Genome Data
Genome Data
Projects
The table below shows all genomes sequenced by the BCM-HGSC.
The main "initial projects" are shown while ongoing efforts to "upgrade" sequences or identify genetic variation are described later. An important contribution of the BCM-HGSC is continual development of sequence strategies and software that improve draft assembly quality.
After the human, the rat project showcased the "Combined Assembly" method, where BACs were "skimmed" and combined with WGS. We later developed Clone-Array Pooled Shotgun Sequencing (CAPSS) that greatly simplified introduction of BAC components.
With the Sea Urchin and Bovine projects, CAPSS integrated with Combined Assembly became a routine production tool.
| Species | Size | Goal | Sequencing | Project Status | Methods | % BCM |
|---|---|---|---|---|---|---|
| Human (H. sapiens) | 2.9 Gb | Finished | Complete | Complete | Clone by clone | 10.5 |
| Mouse (M. musculus) | 2.6 Gb | Finished | Complete | Complete | Clone by clone | <1.0 |
| Rat (R. norvegicus) | 2.8 Gb | Draft | 7x Complete | Complete | Mixed | 50 |
| Fly (D. melanogaster) | 130 Mb | Finished | 10x Complete | Complete | WGS/BAC | 35 |
| Fly (D. pseudoobscura) | 130 Mb | Draft | 8x Complete | Complete | WGS | 100 |
| Fly (D. pmelanogaster -multiple strains) | 200 Mb | Draft | In progress | In progress | WGS | 100 |
| Honey bee (A. mellifera) | 238 Mb | Draft | 7x Complete | Complete | WGS | 100 |
| cDNAs (H. sapiens) | 12,000 | Finished | N/A | Complete | CCS | 30 |
| cDNAs (M. musculus) | 10,000 | Finished | N/A | Complete | CCS | 30 |
| Sea urchin (S. purpuratus) | 800 Mb | Draft | 7x Complete | Analysis | WGS/CAPSS | 100 |
| Bovine (B. taurus) | 2.9 Gb | Draft | 7x Complete | Analysis | WGS/CAPSS | 100 |
| Rhesus monkey (M. mulatta) | 2.9 Gb | Draft | 5.1x Complete | Analysis | WGS/CAPSS | ~40 |
| Orangutan (P. pygmaeus) | 2.9 Gb | Draft | 6x Complete | Assembly | WGS | 50 |
| Marmoset (C. jacchus) | 2.9 Gb | Draft | 7x Complete | Assembly | WGS | 50 |
| Pea aphid (A. pisum) | 540 Mb | Draft | In progress | In progress | WGS | 100 |
| Wasp (Nasonia spp.) | 330 Mb | Draft | In progress | In progress | WGS | 100 |
| Beetle (T. castaneum) | 155 Mb | Draft | 7x Complete | Analysis | WGS | 100 |
| Wallaby (M. eugenii) | 3.6 Gb | 2x Draft | In progress | In progress | WGS | 50 |
| Acorn worm (S. kowalevskii) | 1.1 Gb | Draft | In progress | In progress | WGS | 100 |
| Hyrax (P. capensis) | 2.9 Gb | 2x | In progress | In progress | WGS | 100 |
| Megabat (P. vampyrus) | 2.9 Gb | 2x Draft | In progress | In progress | WGS | 100 |
| Armadillo (D. novemcinctus) | 3 Gb | Draft | 6x | In progress | WGS | 66 |
| Baboon (P. anubis) | 3 Gb | Draft | 6x | In progress | WGS | 100 |
| Bumble bee (B. terrestris) | 300 Mb | Draft | 15x | In progress | WGS | 100 |
| California mouse (P. californicus) | 3 Gb | Draft | 2x | In progress | WGS | 100 |
| Centipede (S. maritima) | 300 Mb | Draft | 6x | In progress | WGS | 100 |
| Cotton bollworm (H. armigera) | 500 Mb | Draft | 15x | In progress | WGS | 100 |
| Deer mouse (P. maniculatus) | 3 Gb | Draft | 6x | In progress | WGS | 100 |
| Gibbon, Northern white-cheeked (N. leucogenys) | 3 Gb | Draft | 6x | In progress | WGS | 50 |
| Dolphin, Bottlenose (T. truncatus) | Draft | 2.5x | In progress | WGS | 100 | |
| Dwarf honey bee (A. florea) | 300 Mb | Draft | 15x | In progress | WGS | 100 |
| Hessian fly (M. destructor) | 200 Mb | Draft | 15x | In progress | WGS | 100 |
| Kangaroo rat (D. ordii) | 3 Gb | Draft | 2x | In progress | WGS | 100 |
| Lemur, Gray Mouse (M. Murinus) | 3 Gb | Draft | 6x | In progress | WGS | 66 |
| Oldfield mouse (P. polionotus) | 3 Gb | Draft | 2x | In progress | WGS | 100 |
| Sandfly (L. longipalpis) | 300 Mb | Draft | 15x | In progress | WGS | 100 |
| White-footed mouse (P. leucopus) | 3 Gb | Draft | 2x | In progress | WGS | 100 |
Table: Genomes at the BCM-HGSC, past and present. Finished = Bermuda standard; Draft = deep draft coverage >6x of raw data; Mixed = WGS + BAC clone approach; WGS = whole genome shotgun; CCS = Concatenated cDNA Sequencing; CAPSS = Clone Array Pool Shotgun Sequencing; PGI = Pooled Genome Indexing.