Identification of Clade-wide Cis-regulatory Elements from Conserved Non-coding Elements in Cucurbitaceous Genomes

Graphic Abstract

The 12 related genomes

Figure 1. Phylogenetic tree of species included in the 12-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.The topology of 12 species tree were constructed based 12-way whole genome alignments dataset by UPGMA method

Table 1. Genome data source

Species Assembly Name Annotation Release Release Date URL
Cucumis sativus V3 V3 2019/06/18 http://cucurbitgenomics.org/ftp/genome/cucumber/Chinese_long/v3
Cucumis melo V3.6.1 V4 2018/05/24 ftp://cucurbitgenomics.org/pub/cucurbit/genome/melon/v3.6.1/
Citrullus lanatus V2 V2 2019/11/01 http://cucurbitgenomics.org/ftp/genome/watermelon/97103/v2/
Lagenaria siceraria V1 V1 2017/09/23 ftp://cucurbitgenomics.org/pub/cucurbit/genome/Lagenaria_siceraria/
Benincasa V1 V1 2019/11/14 http://cucurbitgenomics.org/ftp/genome/wax_gourd/
Curcurbita maxima V1.1 V1.1 2017/09/14 ftp://ftp.ncbi.nlm.nih.gov/genomes/Malus_domestica
Cucurbita moschata V1 V1 2017/09/14 ftp://cucurbitgenomics.org/pub/cucurbit/genome/Cucurbita_moschata/
Cucurbita pepo V4.1 V4.1 2017/11/07 ftp://cucurbitgenomics.org/pub/cucurbit/genome/Cucurbita_pepo/
Momordica charantia V1 V1 2020/06/23 https://ddbj.nig.ac.jp/public/ddbj_database/wgs/BL/BLBB.gz
Cucurbita argyrosperma V2 V2 2019/04/01 http://cucurbitgenomics.org/ftp/genome/Cucurbita_argyrosperma/
Sechium edule V1 V1 2021/01/31 http://cucurbitgenomics.org/ftp/genome/chayote/
Luffa cylindrica V1 V1 2020/08/01 https://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Luffa_aegyptiaca/latest_assembly_versions/GCA_017139565.1_ASM1713956v1/