An updated functional annotation of protein-coding genes in the cucumber genome

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