Genome-wide identification, phylogenetic analysis, and expression profiling of ATP-binding cassette transporters in oomycete

Abstract

Abstract Background： ABC transporters are a special family of membrane proteins and fulfill a multitude of functions. In plants, a few research have found ABC transporters acting as virulence factors in oomycete-plant interactions. However, previous studies have only focused on phylogenetic analysis of ABC transporters in particular species, and a comprehensive analysis has not been carried out. In this study, we examined 21 species genomes of oomycetes for phylogenetic and functional analysis of ABC transporters. Aim to find potential virulence factors in the interaction of plants and oomycetes. Result：We identified 29~151 ABC transporter proteins in 21 species of oomycetes, and 965 were filtered in a phylogenetic analysis. The number of ABC transporters in biotrophic oomycetes was significantly lower than in hemi-biotrophic and necrotrophic oomycetes, and the number in Phytophthora was the largest. Our analysis demonstrated that most oomycete ABC transporters are highly conserved, while others show remarkable group-specific diversification. The ABCA group III and ABCB half-size II proteins clustered with bacteria, appearing to be derived from horizontal transfer events from bacterial genomes. The ABCG subfamily was the most expanded group in oomycetes. The number of ABCD subfamily members was the smallest and was highly conserved in oomycetes. The structural characteristics of ABC proteins indicate diverse structural types in each of the ABC subfamilies. A heatmap was used to analyze the expression of ABC transporters. ABC transporters were expressed in middle and late stages, which represent biotrophic and necrotrophic phases, with the exception of some ABCB transporters being highly expressed in early stage. This suggests that ABC proteins expressed in middle and late stages may participate in host disease and cause host cell death. Conclusions: In this study, 965 proteins were filtered in a phylogenetic analysis from 21 species of oomycete representing three different lifestyles. Meanwhile, we also analysis of oomycete ABC proteins provides insight into the diversity of the five subfamilies among the main oomycete lineages. This study presents the first comprehensive overview of the ABC transporter family, and provides an important platform for in-depth analysis of oomycete-plant interactions and a database for identifying pathogenic factors in oomycetes.