博文
Crop Genome Advanced
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Unitl now. about 31 crop species have been published. Average genome size is about 1.5Gb, most of the genome is
below 2Gb. With all of the crop reference genome informations and the genotyping become less cost.Such as Next-generationsequencing technologies which have brought the revolutionary change in biologyresearch，including the analysis of evolution research; genetic mapping; and molecular breeding.
| Species | Genome | Ploidy | Sequence | Publication | Assembly features |
| (common name) | size | strategy | date | ||
| Oryza sativa | 389 Mb | 2n = 2x = 24 | BAC physical map, | Aug-05 | Essentially complete chromosome arm |
| (rice) | Sanger sequencing | coverage | |||
| Populus trichocarpa | 550 Mb | 2n = 2x = 38 | BAC physical map, | Sep-06 | 2,447 cscaffolds containing 410 Mb, 82% of |
| (black cottonwood) | WGS, Sanger sequencing | sequence genetically anchored | |||
| Vitus vinifera | 475 Mb | 2n = 2x = 36 | WGS, Sanger | Sep-07 | 3,514 csupercontigs containing 487 Mb, 69% of |
| (pinot noir grape) | sequencing | sequence genetically anchored | |||
| Sorghum bicolor | 700 Mb | 2n = 2x = 20 | WGS, Sanger | Jan-09 | 229 scaffolds containing 97% of the genome, |
| (sorghum) | sequencing | 88% of sequence genetically anchored | |||
| Zea mays | 2,300 Mb | 2n = 2x = 20, | BAC physical map, | Nov-09 | 2,048 Mb in 125,325 bp contigs forming 61,161 scaffolds |
| (maize) | one aWGD | BAC sequence 4-6 x | |||
| allotetraploid | deep | ||||
| Glycine max | 1,115 Mb | Two WGD | WGS, Sanger | Jan-10 | 397 scaffolds containing 85% of the genome, |
| (soybean) | 2n = 2x = 40 | sequencing | 98% of sequence genetically anchored | ||
| allopolyploid | |||||
| Malus x domestica | 750 Mb | One WGD | WGS, Sanger, Roche | Oct-10 | 1,629 cmetacontigs containing 80% of the |
| (apple) | 2n = 2x = 34 | 454 | genome, 71% of sequence genetically anchored | ||
| Theobroma cacao | 430 Mb | 2n = 2x = 20 | WGS, Sanger, | Dec-10 | 524 scaffolds containing 80% of the genome, |
| (cacao) | Illumina, Roche 454 | 67% of sequence genetically anchored | |||
| Fragaria vesca | 240 Mb | 2n = 2x = 14 | WGS, Roche 454, | Dec-10 | 272 scaffolds containing 95% of the genome, |
| (woodland | Illumina, SOLiD | 94% of sequence genetically anchored | |||
| strawberry) | |||||
| Phoenix dactylifera | 658 Mb | 2n = 2x = 36 | WGS, Illumina | Jun-11 | 57,277 scaffolds containing 60% of the |
| (date palm) | genome | ||||
| Solanum tuberosum | 844 Mb | 2n = 4x = 48 | Double monoploid | Jul-11 | 443 superscaffolds containing 78% of the |
| (potato) | DM and diploid RH, | genome, 86% of the assembly genetically | |||
| WGS, Illumina, Roche 454 | anchored | ||||
| Brassica rapa | 485 Mb | Three WGD | WGS, Illumina, | Aug-11 | 288 Mb in scaffolds, 90% of the assembly |
| (Chinese cabbage) | 2n = 2x = 20 | BAC end Sanger sequencing | genetically anchored | ||
| Medicago truncatula | 375 Mb | WGD | BAC physical map, | Dec-11 | 8 pseudomolecules containing 70% of the |
| (alfalfa relative) | 2n = 2x = 16 | Sanger, Illumina | genome, 100% in optical map | ||
| Manihot esculenta | 770 Mb | 2n = 2x = 36 | WGS, Roche 454, | Jan-12 | 12,977 scaffolds containing 80% of the |
| (cassava) | BAC end Sanger sequencing | genome | |||
| Cajanus cajan | 833 Mb | 2n = 2x = 22 | WGS, Illumina | Jan-12 | 137,542 scaffolds containing 73% of the |
| (pigeonpea) | genome | ||||
| Setaria italic | 500 Mb | 2n = 2x = 18 | WGS, Sanger, | May-12 | 597 scaffolds containing 80% of the genome, |
| (foxtail millet) | Illumina, BAC end sequence | 99% of the assembly genetically anchored | |||
| Solanum lycopersicum | 900 Mb | 2n = 2x = 24 | WGS, Roche 454, | May-12 | 91 scaffolds containing 85% of the genome, |
| (tomato) | Illumina and SOLiD, BAC end Sanger sequencing | 99% of the assembly genetically anchored | |||
| Cucumis melo | 312 Mb | Three WGD | WGS, Roche 454, BAC | Jul-12 | 1,584 scaffolds containing 83% of the genome, |
| (melon) | 2n = 2x = 24 | end sequencing | 88% of the assembly genetically anchored | ||
| Musa acuminate | 523 Mb | 2n = 2x = 22 | WGS, Roche 454, | Aug-12 | 24,425 contigs containing 90% of the genome, |
| (Cavendish banana) | Sanger, Illumina | 70% of the assembly genetically anchored | |||
| Citrus sinensis | 367 Mb | 2n = 2x = 18 | Dihaploid WGS, | Jan-13 | 4,811 scaffolds containing 82% of the genome, |
| (Valencia sweet | Illumina | 73% of the assembly genetically anchored | |||
| orange) | |||||
| Gossypium raimondii | 880 Mb | 2n = 2x = 26 | WGS, Illumina | Aug-12 | 4,715 scaffolds containing 85% of the genome, |
| (D genome cotton) | 73% of the assembly genetically anchored | ||||
| Hordeum vulgare | 5,100 Mb | 2n = 2x = 14 | WGS, Illumina, | Nov-12 | Physical map (4.98 Gb), BAC sequence |
| (barley) | BAC physical map, | (1.13 Gb), WGS assemblies (1.9 Gb); integrated | |||
| BAC sequence | by physical map and syntenic order | ||||
| (Roche 454, Illumina) | |||||
| Triticum aestivum | 17,000 Mb | 2n = 6x = 42 | WGS, Roche 454 | Nov-12 | Orthologous group assembly, 437 Mb |
| (bread wheat) | allopolyploid | ||||
| Gossypium raimondii | 880 Mb | 2n = 2x = 26 | WGS, Sanger, | Dec-12 | 1,084 scaffolds containing 86% of the genome, |
| (D genome cotton) | Roche 454, Illumina | 98% anchored and oriented to genetic map | |||
| G. hirsutum | AtDt | Illumina | 82x coverage | ||
| (upland cotton) | allopolyploid | ||||
| Cicer arietinum | 738 Mb | 2n = 2x = 16 | WGS, Illumina | Jan-13 | 7,163 scaffolds containing 64% of the genome |
| (chickpea) | BAC end sequence | ||||
| Phylostachys | 2 Gb | 2n = 2x = 48 | WGS, Illumina | Apr-13 | 80% of the 2.05 Gb assembly maps to 5,499 |
| heterocycla | BAC end sequence | scaffolds of less than 62 kb | |||
| (bamboo) | |||||
| Picea abies | 20,000 Mb | 2n = 2x = 24 | fosmid pools with | May-13 | Merged assembly 12.0 Gb, with 4.3 Gb in |
| (Norway spruce) | both haploid | ≥10 kb scaff olds | |||
| (megagametophyte) | |||||
| and diploid WGS | |||||
| Pinus taeda | 24,000 Mb | 2n = 2x = 24 | WGS single haploid | In progress | |
| (Loblolly pine) | megagametophyte | ||||
| assembly | |||||
| Miscanthus sp. | 1,500 Mb | One WGD, | WGS | In progress | |
| (elephant grass) | diploid | ||||
| progenitors | |||||
| 2n = 2x = 38 | |||||
| Elais guineensis Elais oleifera(oil palm) | 1,890 Mb | 2n = 2x = 32 | WGS, BAC physical | In progress | |
| commercial F1 | maps | ||||
| hybrids | |||||
| Saccharum | >15,000Mb | Diploid | WGS | In progress | |
| officinarum x | progenitors | ||||
| S. spontaneum | x = 10; 2n = 80; | ||||
| (sugar cane) | x = 8; | ||||
| 2n = 40-128 |
https://blog.sciencenet.cn/blog-491809-690696.html
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