Genome-Wide Identification and Expression Analysis of the VILLIN Gene Family in Soybean

Abstract

The VILLIN (VLN) protein is an important regulator of the actin cytoskeleton, which orchestrates many developmental processes and participates in various biotic and abiotic responses in plants. Although the VLN gene family and their potential functions have been analyzed in several plants, knowledge of VLN genes in soybeans and legumes remains rather limited. In this study, a total of 35 VLNs were characterized from soybean and five related legumes. Combining with the VLN sequences from other nine land plants, we categorized the VLN gene family into three groups according to phylogenetic relationships. Further detailed analysis of the soybean VLNs indicated that the ten GmVLNs were distributed on 10 of the 20 chromosomes, and their gene structures and protein motifs showed high group specificities. The expression pattern analysis suggested that most GmVLNs are widely expressed in various tissues, but three members have a very high level in seeds. Moreover, we observed that the cis−elements enriched in the promoters of GmVLNs are mainly related to abiotic stresses, hormone signals, and developmental processes. The largest number of cis−elements were associated with light responses, and two GmVLNs, GmVLN5a, and GmVLN5b were significantly increased under the long light condition. This study not only provides some basic information about the VLN gene family but also provides a good reference for further characterizing the diverse functions of VLN genes in soybeans.

Genome-Wide Analysis of VILLIN Gene Family Associated with Stress Responses in Cotton (Gossypium spp.)

“…Additionally, 20 sequences were identified, the majority of which belong to the ADF and gelsolin superfamily ( Table 1 ) ( Figure 7 B). These structural configurations align with the findings of previous studies [ 56 , 57 ].…”

“…The protein–protein interaction revealed that GhVLN proteins interact with various cytoskeletal proteins, hence playing a crucial role in stress responses ( Figure 10 ). This observation implies that these genes likely play crucial roles in response to stress, aligning with similar findings in other species [ 56 , 57 ]. This outcome is in line with findings from other studies, where AtVLNs exhibited distinct expression patterns featuring elevated expression levels and a preference for specific tissues [ 59 ].…”

“…The collinearity analysis using the Arabidopsis genome suggested that the synteny between the GhVLN gene and Arabidopsis may share a common ancestor during its evolution ( Figure 8 A). The 3D-structure prediction suggested that the GhVLNs exhibit similar spatial structures which were consisted with previous studies on Glycine max [ 57 ]. Furthermore, we employed protein–protein interaction and cis-element analysis to assess the gene expression pattern within the promoter region [ 58 ].…”

Research progress on the roles of actin-depolymerizing factor in plant stress responses

“…In contrast to single-cell eukaryotes and animals, plants exhibit a multitude of distinct and functionally specialized actin filament systems, alongside a larger actin gene family ( McDowell et al., 1996 ; Zhang et al., 2010 ; Gunning et al., 2015 ). Likewise, an increased number of genes has been observed in numerous ABP gene families, such as profilin, formin, and villin ( Bao et al., 2011 ; Gunning et al., 2015 ; Duan et al., 2021 ; Zhou et al., 2023 ). The diverse members within these extensive gene families, believed to have originated from gene duplication events, are presumed to be expressed in a highly differential manner, specific to tissues, environmental conditions, and temporal factors ( McDowell et al., 1996 ; Bao et al., 2011 ).…”