Data for Global Convergence of Molecular Evolution in Root Flora
Description
The compressed file RootFlora.zip contains the specified directories and relevant files detailed below: 1. 205species This folder includes TD-, WGD- and HGT-derived genes, gene families, and Ks values of TD-derived gene pairs in each of 205 studied species. 2. Ancestral_and_specific_TD_events Ancestral and independent TD events in Arabidopsis thaliana, Schrenkiella parvula, Oryza sativa and Zizania latifolia. The TD events that occurred before and after the divergence of A. thaliana and S. parvula, as well as O. sativa and Z. latifolia, were considered ancestral and specific TD events, respectively. 3. Biotic_stress List of upregulated genes in Arabidopsis thaliana and Oryza sativa and under biotic stresses, such as Botrytis cinereal, Colletotrichum tofieldiae, flg22, Heterodera schachti nematodes, Heterodera schachtii parasitism, Pseudomonas syringae, Rhizobium sp, and Verticillium dahlia on Arabidopsis thaliana and Meloidogyne incognita, Magnaporthe oryzae, Azospirillum brasilense, Soil microbiome, Hirschmanniella oryzae, Rhizophagus irregularis, Burkholderia vietnamiensis and Paraburkholderia kururiensis on Oryza sativa. 4. GLM_analysis The details of the species geographical coordinates, climatic, anthropogenic, edaphic, and plant morpho-ecospace variables, and the GLM analysis results of 1000 bootstrap resampling replicates. 5. GO_enrichment The GO term annotations for 28 representative species and enriched terms of TD- and WGD-derived family genes. 6. MLtree The original phylogenetic tree files for the ten TD-derived families. The phylogenetic trees were constructed using 17 representative plants, including Rhodophytes (Galdieria sulphuraria and Gracilariopsis chorda), Prasinodermophyta (Prasinoderma coloniale), Chlorophytes (Chlamydomonas reinhardtii and Chloropicon primus), Charophytes (Klebsormidium nitens and Mesotaenium endlicherianum), Bryophytes (Marchantia polymorpha and Anthoceros angustus), Lycophytes (Isoetes taiwanensis and Selaginella moellendorffii), Ferns (Adiantum capillus-veneris and Alsophila spinulosa), Gymnosperms (Torreya grandis and Pinus lambertiana), and Angiosperms (Arabidopsis thaliana and Oryza sativa). 7. Mangroves The details of 15 mangrove genomes. You can obtain gene lists of TD-derived genes, gene families, and Ks values of TD-gene pairs in each mangrove species form this folder. 8. Code The code used in this study, including 'HGTdetector.sh' and other scripts.