Genome-wide identification of the glutamate receptor-like gene family in Vanilla planifolia and their response to Fusarium oxysporum infection

Abstract

Glutamate receptor-like genes (GLRs) are essential for plant growth and development and for coping with environmental (biological and non-biological) stresses. In this study, 13 GLR members were identified in the Vanilla planifolia genome and attributed to two subgroups (Clade I and Clade III) based on their physical relationships. Cis-acting element analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated the GLR gene regulation's complexity and their functional diversity. Expression analysis revealed a relatively higher and more general expression pattern of Clade III members compared to the Clade I subgroup in tissues. Most GLRs showed significant differences in expression during Fusarium oxysporum infection. This suggested that GLRs play a critical role in the response of V. planifolia to pathogenic infection. These results provide helpful information for further functional research and crop improvement of VpGLRs.

Keywords: Fusarium oxysporum; Vanilla planifolia; biotic stress; expression pattern; glutamate receptor-like genes.

Figure 1.

Phylogenetic tree of GLR proteins from Arabidopsis, rice, and soybean. All protein sequences were aligned using MAFFT and the maximum likelihood (ML) tree was constructed using IQtree with 1,000 bootstrap replicates. Different colors indicate distinct subgroups or species.

Figure 2.

Schematic diagram of the phylogenetic tree (a); conserved motif (b); and gene structure (c) of VpGlrs. Genes from the same subtribe were indicated by the same color.

Figure 3.

Chromosomal distribution of GLR genes in Vanilla planifolia. Chromosome size is indicated by its relative length. Chromosome numbers are shown at the left of each chromosome.

Figure 4.

Genome-wide synteny analysis of GLRs between Vanilla planifolia, Oryza sativa, and Arabidopsis thaliana. GLRs and chromosomes from the different species were indicated by the different colors.

Figure 5.

The distribution of cis-acting regulatory elements in the promoters of the VpGLR gene family members.

Figure 6.

Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of VpGlrs. (a) Highly enriched GO terms in VpGlrs; (b) highly enriched KEGG pathways in VpGlrs.

Figure 7.

Expression profiles of VpGLR genes. (a) Expression pattern of VpGLR genes in different tissues at six months; (b) Expression pattern of VpFAD genes for Fusarium oxysporum-infected roots after 12 weeks of room-temperature culture. “C-2d” denotes untreated by F. oxysporum at two days control group (uninfected group); “C-10d” means untreated by F. oxysporum at ten days control group (uninfected group); “I-2d” represents the infected group at two days after F. oxysporum treatment; “I-10d” indicates the infected group at ten days after F. oxysporum treatment.