Abstract
BackgroundDomain 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.ResultsIn 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.ConclusionThese 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.
Highlights
Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes
Seven segmental duplications events involving 14 ATDUF4228 genes (AT1G06980/AT2G30230, AT1G10530/AT1G60010, AT1G21010/AT1G76660, AT2G23690/AT4G37240, AT3G0 3280/AT5G17350, AT3G10120/AT5G03890 and AT3G508 00/AT5G66580) were identified, but no tandemly duplicated gene pairs were found. These results indicated that some ATDUF4228 genes may have been generated by gene duplication and that segmental duplication events represent a major driving force of ATDUF4228 evolution
In this study, 489 DUF4228 genes were identified in 14 high-quality genomes of land plants for the first time, and a comprehensive analysis of phylogenetic relationships and conserved motifs was carried out
Summary
Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. Domains of unknown function (DUFs) are a large set of families within the Pfam database that do not include any proteins of known function [1]. A DUF family will be renamed when the function of at least one of its members has been experimentally determined, but the number of newly added DUFs is much greater than that of renamed DUFs due to the development of sequencing technology [4]. Comprehensive genomic analysis enables researchers to understand the origin, evolution, and biological functions of a gene family. There have been numerous reports on other gene families in plants, there have been few reports of comprehensive genomic analyses of DUF families. Such analyses have been reported for DUF221, DUF810, DUF866, DUF936 and DUF1618 from Oryza sativa [8,9,10,11,12], the DUF481 and DUF724 gene families from Arabidopsis thaliana [13, 14], and DUF1313 genes from 81 photoautotrophic species [6]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
