Phylogenetic Analysis of VcWOX Genes in Relation to Other Plant Species

This study aimed to determine the phylogenetic relationship between VcWOX genes and WOX genes found in various other plant species. To achieve this, we retrieved WOX gene sequences from six different plant species, namely Arabidopsis (15 genes), rice (13 genes), grape (12 genes), white poplar (18 genes), sweet orange (11 genes), and soybean (33 genes) from publicly available databases including NCBI (www.ncbi.nlm.nih.gov), TAIR (www.arabidopsis.org), and RAP-DB (https://rapdb.dna.affrc.go.jp/).

We then performed a multiple sequence alignment of the coding sequences (CDS) of a total of 141 WOX genes using MEGA7 software. This alignment served as the basis for constructing a maximum likelihood tree, which allowed us to infer the evolutionary relationships between the different WOX genes. Our analysis revealed that the WOX genes could be clustered into three distinct groups, designated as groups I, II, and III.

The branches within the phylogenetic tree are labeled with bootstrap values, calculated from 1000 replicates. These values range from 0 to 100, and represent the percentage of times that a particular grouping of genes was observed in the replicate trees. Higher bootstrap values indicate greater confidence in the inferred evolutionary relationship.

To facilitate visual comparison of the different species within the tree, we employed a color-coded symbol scheme. Specifically, we used:

Red triangles: Vaccinium corymbosum * Purple squares: Vitis vinifera* Pink triangles: Populus tomentosa* Green triangles: Glycine max* Yellow triangles: Arabidopsis thaliana* Blue circles: Oryza sativa* Blank triangles: Citrus sinensis

Phylogenetic Analysis of VcWOX Genes in Relation to Other Plant Species