Gradual genomic streamlining and convergent adaptation during terrestrial-to-aquatic transitions in angiosperms

The compressed file GCAA.zip (Gradient Convergence of Aquatic Angiosperms) contains the specified directories and relevant files detailed below:

1. Life_habit_dataset.txt
A comprehensive dataset of angiosperm life habits (aquatic or terrestrial). The growth form (herb or woody) of species was determined through WorldFloraDB (www.worldfloradb.net).

3. plant_megatree.tre
The GBOTB phylogeny (GenBank taxa with a backbone provided by Open Tree of Life version 9.1) (Smith and Brown, 2018). This phylogenetic tree was used for ancestral state reconstruction.

4. FigS1_genus.tree
The phylogenetic tree at the genus level used to infer the number of transitions between aquatic and terrestrial habits.

5. family_test.txt
The gene number in each of the 2,638 non-redundant gene families for each species.

6. 232genefamiliesPCA.txt
Data used for PCA analysis of the 232 gene families contracted in aquatic plants.

7. 232genefamiliesPCA_results.txt
Principal component analysis results of the 232 gene families.

8. Microbial_α-_and_β-diversity.xlsx
Microbial α- and β-diversity of terrestrial and aquatic habitats. We downloaded microbial data, including α- and β-diversity metrics, for 10,432 samples from aquatic habitats (saline and non-saline water) and terrestrial habitats (soil and plant rhizosphere) as reported by Thompson et al. The original source of these samples is the Earth Microbiome Project (EMP) (earthmicrobiome.org). The α-diversity was included using the observed OTUs metric, which represents the number of unique 16S rRNA tag sequences.

9. data_on_Cenozoic.txt
Change in aquatic plant proportion relative to total angiosperms during Cenozoic.

10. Monocots_glm_results.txt
The results of the generalized linear model (GLM) analysis of monocot and non-monocot plants.

11. gene_function_annotation
This folder contains the functional prediction results of 28 aquatic plant genes by DeepGO-SE.

12.Orthogroups_genecounts.txt
Here are the gene counts in each orthogroup across different species.

13. variables_cell
Data on the aquatic plant frequency and geo-environmental variables corresponding to each cell.

14. 232_gene_families_of_non-angiosperms.txt
Gene numbers of the 232 gene families in non-angiosperms.

15. GLM_orthogroups.txt
The results of GLM for orthogroups.

16. Figure_orthogroup_results.docx

17. code.R
The R code used in this study.