The 15 related genomes used
Figure 1. Phylogenetic tree of species included in the 15-way cucumber-based alignment,used to guide MULTIZ merging of pairwise alignments
*The neutral tree is based on 4-fold degenerate sites sampled from Chr1~7 with branch lengths proportional to the indicated scale.
Table 1. Genome data source
| Species | Assembly Name | Annotation Release | Release Date | URL |
|---|---|---|---|---|
| Cucumis sativus | V2.0 | V2 | 2014/08/08 | http://cmb.bnu.edu.cn/Cucumis_sativus_v2.0/index.html |
| Cucumis melo | ASM31304v1 | Release100 | 2012/10/05 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Cucumis_melo |
| Citrullus lanatus | V1 | V1 | 2013/09/21 | ftp://www.icugi.org/pub/genome/watermelon |
| Vitis vinifera | 12X | Release101 | 2014/12/10 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Vitis_vinifera |
| Malus domestica | MalDomGD1.0 | Release100 | 2012/08/16 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Malus_domestica |
| Citrus sinensis | Csi_valencia_1.0 | Release100 | 2012/12/12 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Citrus_sinensis |
| Populus trichocarpa | Poptr2_0 | Poptr2_0 | 2013/10/18 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Populus_trichocarpa |
| Glycine max | V1.1 | Release101 | 2014/01/07 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Glycine_max |
| Solanum tuberosum | SolTub_3.0 | Release100 | 2013/12/12 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Solanum_tuberosum |
| Arabidopsis thaliana | TAIR10 | TAIR10 | 2012/08/22 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Arabidopsis_thaliana |
| Arabidopsis lyrata | V1.0 | V1.0 | 2014/08/11 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Arabidopsis_lyrate |
| Brassica rapa | Brapa_1.0 | Release100 | 2014/09/08 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Brassica_rapa |
| Setaria italic | SetariaV1 | Release100 | 2013/06/26 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Setaria_italic |
| Brachypodium distachyon | V1.0 | Release101 | 2014/12/14 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Bracgypodium |
| Oryza brachyantha | V1.4b | Release100 | 2014/01/14 | ftp://ftp.ncbi.nlm.nih.gov/genomes/Oryza_brachyantha |