Table 1 Progress in crop genome sequencing
Species (common name) | Genome size | Ploidy | Sequence strategy | Publication date | Assembly features | Reference |
|---|---|---|---|---|---|---|
Oryza sativa (rice) | 389 Mb | 2n = 2x = 24 | BAC physical map, Sanger sequencing | Aug 2005 | Essentially complete chromosome arm coverage | [2] |
Populus trichocarpa (black cottonwood) | 550 Mb | 2n = 2x = 38 | BAC physical map, WGS, Sanger sequencing | Sep 2006 | 2,447 cscaffolds containing 410 Mb, 82% of sequence genetically anchored | [3] |
Vitus vinifera (pinot noir grape) | 475 Mb | 2n = 2x = 36 | WGS, Sanger sequencing | Sep 2007 | 3,514 csupercontigs containing 487 Mb, 69% of sequence genetically anchored | [5] |
Sorghum bicolor (sorghum) | 700 Mb | 2n = 2x = 20 | WGS, Sanger sequencing | Jan 2009 | 229 scaffolds containing 97% of the genome, 88% of sequence genetically anchored | [6] |
Zea mays (maize) | 2,300 Mb | 2n = 2x = 20, one aWGD allotetraploid | BAC physical map, BAC sequence 4-6 x deep | Nov 2009 | 2,048 Mb in 125,325 bcontigs forming 61,161 scaffolds | [4] |
Glycine max (soybean) | 1,115 Mb | Two WGD 2n = 2x = 40 allopolyploid | WGS, Sanger sequencing | Jan 2010 | 397 scaffolds containing 85% of the genome, 98% of sequence genetically anchored | [7] |
Malus × domestica (apple) | 750 Mb | One WGD 2n = 2x = 34 | WGS, Sanger, Roche 454 | Oct 2010 | 1,629 cmetacontigs containing 80% of the genome, 71% of sequence genetically anchored | [10] |
Theobroma cacao (cacao) | 430 Mb | 2n = 2x = 20 | WGS, Sanger, Illumina, Roche 454 | Dec 2010 | 524 scaffolds containing 80% of the genome, 67% of sequence genetically anchored | [11] |
Fragaria vesca (woodland strawberry) | 240 Mb | 2n = 2x = 14 | WGS, Roche 454, Illumina, SOLiD | Dec 2010 | 272 scaffolds containing 95% of the genome, 94% of sequence genetically anchored | [13] |
Phoenix dactylifera (date palm) | 658 Mb | 2n = 2x = 36 | WGS, Illumina | June 2011 | 57,277 scaffolds containing 60% of the genome | [12] |
Solanum tuberosum (potato) | 844 Mb | 2n = 4x = 48 | Double monoploid DM and diploid RH, WGS, Illumina, Roche 454 | July 2011 | 443 superscaffolds containing 78% of the genome, 86% of the assembly genetically anchored | [14] |
Brassica rapa (Chinese cabbage) | 485 Mb | Three WGD 2n = 2x = 20 | WGS, Illumina, BAC end Sanger sequencing | Aug 2011 | 288 Mb in scaffolds, 90% of the assembly genetically anchored | [15] |
Medicago truncatula (alfalfa relative) | 375 Mb | WGD 2n = 2x = 16 | BAC physical map, Sanger, Illumina | Dec 2011 | 8 pseudomolecules containing 70% of the genome, 100% in optical map | [16] |
Manihot esculenta (cassava) | 770 Mb | 2n = 2x = 36 | WGS, Roche 454, BAC end Sanger sequencing | Jan 2012 | 12,977 scaffolds containing 80% of the genome | [19] |
Cajanus cajan (pigeonpea) | 833 Mb | 2n = 2x = 22 | WGS, Illumina | Jan 2012 | 137,542 scaffolds containing 73% of the genome | [20] |
Setaria italic (foxtail millet) | 500 Mb | 2n = 2x = 18 | WGS, Sanger, Illumina, BAC end sequence | May 2012 | 597 scaffolds containing 80% of the genome, 99% of the assembly genetically anchored | [21] |
Solanum lycopersicum (tomato) | 900 Mb | 2n = 2x = 24 | WGS, Roche 454, Illumina and SOLiD, BAC end Sanger sequencing | May 2012 | 91 scaffolds containing 85% of the genome, 99% of the assembly genetically anchored | [17] |
Cucumis melo (melon) | 312 Mb | Three WGD 2n = 2x = 24 | WGS, Roche 454, BAC end sequencing | July 2012 | 1,584 scaffolds containing 83% of the genome, 88% of the assembly genetically anchored | [22] |
Musa acuminate (Cavendish banana) | 523 Mb | 2n = 2x = 22 | WGS, Roche 454, Sanger, Illumina | Aug 2012 | 24,425 contigs containing 90% of the genome, 70% of the assembly genetically anchored | [33] |
Citrus sinensis (Valencia sweet orange) | 367 Mb | 2n = 2x = 18 | Dihaploid WGS, Illumina | Jan 2013 | 4,811 scaffolds containing 82% of the genome, 73% of the assembly genetically anchored | [23] |
Gossypium raimondii (D genome cotton) | 880 Mb | 2n = 2x = 26 | WGS, Illumina | Aug 2012 | 4,715 scaffolds containing 85% of the genome, 73% of the assembly genetically anchored | [24] |
Hordeum vulgare (barley) | 5,100 Mb | 2n = 2x = 14 | WGS, Illumina, BAC physical map, BAC sequence (Roche 454, Illumina) | Nov 2012 | Physical map (4.98 Gb), BAC sequence (1.13 Gb), WGS assemblies (1.9 Gb); integrated by physical map and syntenic order | [26] |
Triticum aestivum (bread wheat) | 17,000 Mb | 2n = 6x = 42 allopolyploid | WGS, Roche 454 | Nov 2012 | Orthologous group assembly, 437 Mb | [27] |
Gossypium raimondii (D genome cotton) G. hirsutum (upland cotton) | 880 Mb | 2n = 2x = 26 AtDt allopolyploid | WGS, Sanger, Roche 454, Illumina Illumina | Dec 2012 | 1,084 scaffolds containing 86% of the genome, 98% anchored and oriented to genetic map 82x coverage | [25] |
Cicer arietinum (chickpea) | 738 Mb | 2n = 2x = 16 | WGS, Illumina BAC end sequence | Jan 2013 | 7,163 scaffolds containing 64% of the genome | [31] |
Phylostachys heterocycla (bamboo) | 2 Gb | 2n = 2x = 48 | WGS, Illumina BAC end sequence | Apr 2013 | 80% of the 2.05 Gb assembly maps to 5,499 scaffolds of less than 62 kb | [34] |
Picea abies (Norway spruce) | 20,000 Mb | 2n = 2x = 24 | fosmid pools with both haploid (megagametophyte) and diploid WGS | May 2013 | Merged assembly 12.0 Gb, with 4.3 Gb in ≥10 kb scaffolds | [42] |
Pinus taeda (Loblolly pine) | 24,000 Mb | 2n = 2x = 24 | WGS single haploid megagametophyte assembly | In progress | Â | Â |
Miscanthus sp. (elephant grass) | 1,500 Mb | One WGD, diploid progenitors 2n = 2x = 38 | WGS | In progress | Â | Â |
Elais guineensis Elais oleifera (oil palm) | 1,890 Mb | 2n = 2x = 32 commercial F1 hybrids | WGS, BAC physical maps | In progress | Â | Â |
Saccharum officinarum x S. spontaneum (sugar cane) | >15,000 Mb | Diploid progenitors x = 10; 2n = 80; × = 8; 2n = 40-128 | WGS | In progress |  |  |