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Background  Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The  DUF4228  gene family is one of these families in plants that has not been described previously.    Results  In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation.  To reveal the possible biological functions of these  DUF4228  genes, 25  ATDUF4228  sequences from  Arabidopsis thaliana  were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in  A. thaliana . Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the  ATDUF4228  genes. Expression profiling of the  ATDUF4228  genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some  ATDUF4228  genes are may be involved in the pathways of plant resistance to abiotic stresses.    Conclusion  These results expand our knowledge of the evolution of the  DUF4228  gene family in plants and will contribute to the elucidation of the biological functions of  DUF4228  genes in the future.

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses