Data for manuscript "The convergent genomic dynamism for aquatic adaptation in vascular plants"

In this study, we conducted whole-genome sequencing of eight aquatic plants and investigated the genomic basis of their adaptation to aquatic environments. Here are some datasets used in this study."Taxon_file.xlsx", the species’ full names and abbreviations used in analyses."Supplementary Data.xlsx", the Supplementary Data (Tables) generated in this study. You can see the detailed information about each Supplementary Data."Supplementary_Data_3_Genome_Assembly.zip", the CDSs and PEPs of the eight species we have conducted whole genome sequencing. The assembled genomes and their annotations have been deposited at CNGBdb (https://db.cngb.org/) under BioProject No. CNP0007358."Supplementary_Data_4_122species_peps.7z", the sequences of homologs in the 122 species obtained from the SWIPE search."Supplementary_Data_15_CAFE_lycop_ferns.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "lycophytes and ferns"."Supplementary_Data_16_CAFE_ang_sub.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "angiosperms"."Supplementary_Data_17_CAFE_Seagrasses.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "Alismatales-focused"." Supplementary_Data_24_bait_peps.zip", the PEPs used as "baits" to search for homologs in 122 species with SWIPE."Supplementary_Figs.7-18_swipe_aln_cln_aligned_peps.zip", the aligned sequences of homologs. These files were used to construct maximum likelihood trees (Supplementary Figs. 6–19) and count gene copy numbers (Supplementary Data 15)."Mitochondrial genome assembly and annotation", mitochondrial genome assembly and annotation of the five species generated in this study (Include Zostera japonica, Thalassia hemprichii, Potamogeton crispus, Ottelia alismoides and Tofieldia thibetica).We will make every effort to upload our raw data to public databases, allowing other researchers to benefit from it.If you have any questions, please contact Ling-Yun Chen: lychen@cpu.edu.cn