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Proteins with a domain of unknown function (DUF) represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. In particular, members of the DUF1005 family in plants have a 411-amino-acid conserved domain, and this family has not been described previously. In this study, a total of 302 high-confidence DUF1005 family members were identified from 58 plant species, and none were found in the four algae that were selected. Thus, this result showed that DUF1005s might belong to a kind of plant-specific gene family, and this family has not been evolutionarily expanded. Phylogenetic analysis showed that the DUF1005 family genes could be classified into four subgroups in 58 plant species. The earliest group to emerge was Group I, including a total of 100 gene sequences, and this group was present in almost all selected species spanning from mosses to seed plants. Group II and Group III, with 69 and 74 members, respectively, belong to angiosperms. Finally, with 59 members, Group IV was the last batch of genes to emerge, and this group is unique to dicotyledons. Expression pattern analysis of the CiDUF1005, a member of the DUF1005 family from Caragana intermedia, showed that CiDUF1005 genes were differentially regulated under various treatments. Compared to the wild type, transgenic lines with heterologous CiDUF1005 expression in Arabidopsis thaliana had longer primary roots and more lateral roots. These results expanded our knowledge of the evolution of the DUF1005 family in plants and will contribute to elucidating biological functions of the DUF1005 family in the future.

Additional file 3: Figure S1. Details of the phylogenetic classification of DUF4228 genes in land plant lineages. Phylogenetic tree was constructed using the ML method with IQ-tree. Green lines represent bryophytes, pink lines represent pteridophytes, blue lines represent gymnosperms and red lines represent angiosperms.

Additional file 6: Figure S4. The distribution of ATDUF4228 genes on the chromosomes. The chromosomal position of each ATDUF4228 gene was mapped according to the genome of A. thaliana. The chromosome number is indicated at the top of each chromosome.

Additional file 5: Figure S3. The motif compositions of DUF4228 proteins in plants. Motifs conserved across DUF4228 proteins were identified through MEME analysis.

Additional file 2: Table S2. List of DUF4228 genes included in this study and the features of their encoded proteins. Those DUF4228 proteins with a domain coverage of less than 70% are labelled in yellow. The genes are marked in red because some amino acid residues in their protein sequence are represented by “X”.

Additional file 8: Table S3. Number and location of abiotic stress- and hormone-responsive cis-elements present in the promoter regions of ATDUF4228 genes.

Additional file 7: Figure S5. Exon-intron structure of the ATDUF4228 genes. Yellow boxes: exons; blue boxes: UTRs; black lines: introns. The lengths of the boxes and lines are scaled based on gene length.

Additional file 10: Figure S7. Protein-protein interaction network of ATDUF4228 proteins. In the network generated by STRINGV9.1, each node represents a protein and each edge represents an interaction, coloured by evidence type.

Additional file 11: Table S4. Summary of ATDUF4228 genes with significantly altered expression (fold change≥2) after osmotic, cold and salt treatment. “up” indicates upregulated expression with a minimum 2-fold change compared with the control. “down” indicates downregulated expression with a minimum 2-fold change compared with the control. “-” indicates no obvious change detected.

Additional file 12: Table S5. All primers used in this study.

Additional file 4: Figure S2. Distribution of the DUF4228 domain in the DUF4228 proteins of plants.