Fig. 1

Phylogenetic relationships of protein sequences with the cupin domain PFAM00190 in the genome of rice cultivar Nipponbare. The tree was generated by distance matrix using ClustalX and rooted with spherulin a. The bicupin class contains 25 genes which were all annotated as seed storage proteins. The monocupin class is composed of 45 genes; the annotation of these genes is shown at the right of the figure. Homologous genes physically close to each other are joined by bars or bars joined by brackets. Genes with expression evidence are boldfaced. Genes marked with an asterisk do not belong to any subclass or cluster and are considered as phylogenetic singletons. The values to the left of the subclass are the results of positive selection analyses, where p is the probability value, ω is the dN/dS value under M8 of codeml, and P1 is the inferred proportion of positively selected sites.