Summary: Glycosyltransferases (GTs) (EC 2.4.x.y) catalyze the transfer of sugar moieties to a wide range of acceptor molecules, such as sugars, lipids, proteins, nucleic acids, antibiotics and other small molecules, including plant secondary metabolites. These enzymes can be classified into at least 92 families, of which family 1 glycosyltransferases (GT1), often referred to as UDP glycosyltransferases (UGTs), is the largest in the plant kingdom. To understand how UGTs expanded in both number and function during evolution of land plants, we screened genome sequences from six plants (Physcomitrella patens, Selaginella moellendorffii, Populus trichocarpa, Oryza sativa, Arabidopsis thaliana and Arabidopsis lyrata) for the presence of a conserved UGT protein domain. Phylogenetic analyses of the UGT genes revealed a significant expansion of UGTs, with lineage specificity and a higher duplication rate in vascular plants after the divergence of Physcomitrella. The UGTs from the six species fell into 24 orthologous groups that contained genes derived from the common ancestor of these six species. Some orthologous groups contained multiple UGT families with known functions, suggesting that UGTs discriminate compounds as substrates in a lineage‐specific manner. Orthologous groups containing only a single UGT family tend to play a crucial role in plants, suggesting that such UGT families may have not expanded because of evolutionary constraints.

It is likely that many small ORFs (sORFs; 30–100 amino acids) are missed when genomes are annotated. To overcome this limitation, we identified ∼8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis thaliana genome. However, the question remains as to whether these coding sORFs play functional roles. Using a designed array, we generated an expression atlas for 16 organs and 17 environmental conditions among 7,901 identified coding sORFs. A total of 2,099 coding sORFs were highly expressed under at least one experimental condition, and 571 were significantly conserved in other land plants. A total of 473 coding sORFs were overexpressed; ∼10% (49/473) induced visible phenotypic effects, a proportion that is approximately seven times higher than that of randomly chosen known genes. These results indicate that many coding sORFs hidden in plant genomes are associated with morphogenesis. We believe that the expression atlas will contribute to further study of the roles of sORFs in plants.

Summary: To identify candidate genes involved in Arabidopsis flavonoid biosynthesis, we applied transcriptome coexpression analysis and independent component analyses with 1388 microarray data from publicly available databases. Two glycosyltransferases, UGT79B1 and UGT84A2 were found to cluster with anthocyanin biosynthetic genes. Anthocyanin was drastically reduced in ugt79b1 knockout mutants. Recombinant UGT79B1 protein converted cyanidin 3‐O‐glucoside to cyanidin 3‐O‐xylosyl(1→2)glucoside. UGT79B1 recognized 3‐O‐glucosylated anthocyanidins/flavonols and uridine diphosphate (UDP)‐xylose, but not 3,5‐O‐diglucosylated anthocyanidins, indicating that UGT79B1 encodes anthocyanin 3‐O‐glucoside: 2′′‐O‐xylosyltransferase. UGT84A2 is known to encode sinapic acid: UDP‐glucosyltransferase. In ugt84a2 knockout mutants, a major sinapoylated anthocyanin was drastically reduced. A comparison of anthocyanin profiles in ugt84a knockout mutants indicated that UGT84A2 plays a major role in sinapoylation of anthocyanin, and that other UGT84As contribute the production of 1‐O‐sinapoylglucose to a lesser extent. These data suggest major routes from cyanidin 3‐O‐glucoside to the most highly modified cyanidin in the potential intricate anthocyanin modification pathways in Arabidopsis.

Summary: sORF finder is a program package for identifying small open reading frames (sORFs) with high-coding potential. This application allows the identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and non-synonymous substitution rates. Availability: Online tools and source codes are freely available at http://evolver.psc.riken.jp/ Contact:kohanada@psc.riken.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Significance: Hormone-like peptides derived from small coding genes (<100 amino acids) have not been extensively characterized in relation to abiotic stress tolerance. Focusing on 17 salinity stress-inducible small coding genes in Arabidopsis , we showed that four genes conferred increased salinity stress tolerance when overexpressed in transgenic plants. One of the four genes ( AtPROPEP3 ) was found to induce salinity stress tolerance by treatment with a 13-peptide (KPTPSSGKGGKHN) fragment, providing unique functional evidence for enhanced salinity stress tolerance in plants in response to a peptide treatment. Although the 13-peptide fragment shares homology with known peptides associated with immune response, the other peptides may encode unique hormone-like peptides associated with salinity stress tolerance.