A systematic bioinformatics analysis of small proteins in plants

Small proteins (SPs, <=100 amino acids in length) are prevalent in all prokaryotes and eukaryotes. They are known to perform varieties of relevant functions and participate in regulation of various biological processes. Although integrated studies of SPs in prokaryotes and animals have been carried out, the systematic investigation on plant SPs still remains an unwritten story. This is mainly because of the lack of sequenced whole genomes in plant, which is improving by the sequence data explosion triggered by next generation sequencing. In this study, we extract 37,003 SPs from 13 whole genome sequenced plants, including 3 green algae, 1 bryophyte, 3 monocots and 6 dicots. We mainly analysed the compositional features, conservative relations, enriched functions in different conserved groups, and the functional domain and evolution characteristics of plant SPs. We observed that the majority of SPs (64.20%) are species specific and 89.31% of these species-specific SPs do not match with any gene ontology (GO) functional annotation. It seems that organisms are likely to enrich SPs to exert specialized functions. By grouping SPs on the basis of sequence conservation within lineages, we noticed that SPs perform lineage-specific functions and many corresponding biological functions emerge with the evolution of SPs. The domains probably evolve independently in SPs while change to other cooperation patterns in the long course of evolution. In addition, gene duplication could be the primary force in the evolution of some plant SPs, for example, small nuclear ribonucleoproteins.