Extended Data Fig. 6: Phylogeny of FER and FER-like genes. | Nature Plants

Extended Data Fig. 6: Phylogeny of FER and FER-like genes.

From: Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago

Extended Data Fig. 6: Phylogeny of FER and FER-like genes.The alternative text for this image may have been generated using AI.

Genomes of Aeschynomene evenia, Arabidopsis thaliana, Bauhinia variegate, Lotus japonicus, Lupinus albu, Medicago truncatula, Oryza sativa, Phaseolus lunatus, Populus trichocarpa and Vitis vinifera were selected, representing species ranging from monocots, basal core eudicots, to legumes. Protein sequences of the orthologs of AtFER (AT3G51550.1) and AtFER-like genes were aligned using mafft-linsi, which were then converted to codon alignments of nucleotide sequences using pal2nal and used to infer phylogenetic relationship with maximum-likelihood approach using RAxML with bootstrap set to 100. Midpoint rooting were performed wiht FigTree and long branches were cut with TreeShrink with quantile set to 0.1. Speciation nodes and duplication nodes were identified with Duplication-Loss-Coalescence Model of dlcpar using species topology extracted from Tree of Life 2.0 with parameter "search". Genes connected via duplication nodes to AtFER were considered as AtFER paralogs and genes connected to AtFER absent of duplication nodes were considered as AtFER orthologs. The final reconciled tree was illustrated with iTOL. Duplication nodes were marked with black dots. The FER clade is highlighted in light red and AtFER and MtFER (Medtr7g073660.1) are highlighted in red and bold.

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