Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum

PeerJ. 2021 Dec 22;9:e12689. doi: 10.7717/peerj.12689. eCollection 2021.


The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.

Keywords: Gene family; Genome-wide analysis; Phosphate ions (Pi) nutrition; SPX; Solanum lycopersicum.

Grant support

This work was supported by the Initial Scientific Research Fund for Dr in Nanchang Normal University (No. NSBSJJ2018032) and the Science and Technology Research Project of Jiangxi Provincial Department of Education (No. GJJ181081). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.