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

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."Supplementary_Data_3_Genome_Assembly.zip", the CDSs and PEPs of the eight species we have conducted whole genome sequencing."Supplementary_Data_4_CAFE_lycop_ferns.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "lycophytes and ferns"."Supplementary_Data_5_CAFE_ang-sub.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "angiosperms"."Supplementary_Data_6_CAFE_Seagrasses.zip", the CDSs and PEPs of the species used for CAFE analyses in the group "Alismatales-focused"."Supplementary_Data_14_bait_peps.zip", the PEPs used as "baits" to search for homologs in 122 species with SWIPE."Supplementary_Data_15_swipe_peps.zip", the PEPs of the 122 species used for homologs search."swipe_peps.7z", the sequences of homologs in the 122 species obtained from the SWIPE search."Supplementary_Figs.6–19_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.<br>Raw reads of 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 (<i>Cabomba caroliniana</i>), PRJNA1244806 (<i>Phyllospadix japonicus</i>), PRJNA1245278 (<i>Zostera japonica</i>), PRJNA1253080 (<i>Thalassia hemprichii</i>), PRJNA1246144 (<i>Potamogeton crispus</i>), PRJNA1246781 (<i>Thalia dealbata</i>), PRJNA1248711 (<i>Juncus effusus</i>), PRJNA1253374 (<i>Myriophyllum spicatum</i>). Raw transcriptome reads for <i>Nymphoides indica</i> and <i>M. spicatum</i> have been deposited in the SRA under BioProject numbers PRJNA1253361 and PRJNA1253374. The assembled genomes and their annotations have been deposited at CNGBdb (https://db.cngb.org/) under BioProject No. CNP0007358.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 Lingyun Chen: [e-mail]