Data for manuscript "Integrated multi-dimensional approaches reveal adaptations of vascular plants to aquatic environments"

In this study, we have conducted whole-genome sequencing for eight aquatic plants and investigated the genomic basis of adaptation to aquatic environments. Here are some datasets used in this study."bait_peps.zip", the protein sequences of bait genes. These sequences were used for the SWIPE search. This dataset corresponds to Supplementary Data 14."swipe_peps.7z", the sequence of homologs in all species generated from the SWIPE search."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)."Taxon_file.xlsx", the species' full names and abbreviations used in analyses.Raw reads of the genome survey, HiFi, HiC, and transcriptome sequencing of the eight species have been deposited in the NCBI Sequence Read Archive (SRA) under the following BioProject numbers: PRJNA1253170 (Cabomba caroliniana), PRJNA1244806 (Phyllospadix japonicus), PRJNA1245278 (Zostera japonica), PRJNA1253080 (Thalassia hemprichii), PRJNA1246144 (Potamogeton crispus), PRJNA1246781 (Thalia dealbata), PRJNA1248711 (Juncus effusus), PRJNA1253374 (Myriophyllum spicatum). Raw transcriptome sequencing reads for Nymphoides indica and M. spicatum have been deposited in the SRA under BioProject numbers: PRJNA1253361 and PRJNA1253374, respectively. The assembled genomes and their annotations of the eight species have been deposited in CNGBdb (https://db.cngb.org/) under BioProject No. CNP0007193.We will make every effort to upload our raw data to public databases so that other researchers can benefit from it.If you have any questions, please contact Lingyun Chen: [e-mail]