Expression profiling and integrative analysis of the CESA/CSL superfamily in rice

<p>Abstract</p> <p>Background</p> <p>The cellulose synthase and cellulose synthase-like gene superfamily (<it>CESA</it>/<it>CSL</it>) is proposed to encode enzymes for cellulose and non-cellulosic matrix polysaccharide synthesis in plants. Although the rice (<it>Oryza sativa </it>L.) genome has been sequenced for a few years, the global expression profiling patterns and functions of the <it>OsCESA</it>/<it>CSL </it>superfamily remain largely unknown.</p> <p>Results</p> <p>A total of 45 identified members of <it>OsCESA</it>/<it>CSL </it>were classified into two clusters based on phylogeny and motif constitution. Duplication events contributed largely to the expansion of this superfamily, with Cluster I and II mainly attributed to tandem and segmental duplication, respectively. With microarray data of 33 tissue samples covering the entire life cycle of rice, fairly high <it>OsCESA </it>gene expression and rather variable <it>OsCSL </it>expression were observed. While some members from each <it>CSL </it>family (<it>A1</it>, <it>C9</it>, <it>D2</it>, <it>E1</it>, <it>F6 </it>and <it>H1</it>) were expressed in all tissues examined, many of <it>OsCSL </it>genes were expressed in specific tissues (stamen and radicles). The expression pattern of <it>OsCESA</it>/<it>CSL </it>and <it>OsBC1L </it>which extensively co-expressed with <it>OsCESA</it>/<it>CSL </it>can be divided into three major groups with ten subgroups, each showing a distinct co-expression in tissues representing typically distinct cell wall constitutions. In particular, <it>OsCESA1, -3 & -8 </it>and <it>OsCESA4, -7 & -9 </it>were strongly co-expressed in tissues typical of primary and secondary cell walls, suggesting that they form as a cellulose synthase complex; these results are similar to the findings in <it>Arabidopsis</it>. <it>OsCESA5</it>/<it>OsCESA6 </it>is likely partially redundant with <it>OsCESA3 </it>for OsCESA complex organization in the specific tissues (plumule and radicle). Moreover, the phylogenetic comparison in rice, <it>Arabidopsis </it>and other species can provide clues for the prediction of orthologous gene expression patterns.</p> <p>Conclusions</p> <p>The study characterized the <it>CESA</it>/<it>CSL </it>of rice using an integrated approach comprised of phylogeny, transcriptional profiling and co-expression analyses. These investigations revealed very useful clues on the major roles of <it>CESA</it>/<it>CSL</it>, their potentially functional complement and their associations for appropriate cell wall synthesis in higher plants.</p