Lgr4 inactivation in mice leads to severe developmental deficiencies in multiple organs

onse to infection by Phytophthora sojae and soybean rust, respectively. Consistent with the expected redundant and overlapping functions of PKs, we found that various subfamilies, specifically those belonging to the same groups, responded similarly to different stress conditions, pointing to common signalling pathways controlled by these subfamilies. interconnectivity of these subfamilies implied their association with specific developmental processes. The stress response co-expression network contained 76 nodes and 364 edges. Finally, when we compared the tissue and stress response co-expression networks we identified 22 subfamilies with 44 co-expression events that were common, suggesting a role for these subfamilies in coordinating developmental processes and stress signalling. Discussion Our genome-wide bioinformatic analysis identified 2166 putative soybean PKs, which represents 4.67 PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19812222 % of all proteincoding genes in the genome. This proportion is higher than that of Arabidopsis, maize, and rice . The size of the soybean PK superfamily is also apparently among the largest in plants. For example, There are 1008 PKs in Arabidopsis, 911 members in M. truncatula, 1417 members in rice, and 1241 members in maize. The large size of the soybean PK superfamily could partly be attributed to the large genome size and two WGD events that occurred 59 and 13 Mya. In addition, high retention of duplicate genes could be another contributing factor. In fact, about 75% of the 46 430 protein-coding genes predicted in soybean were found in multiple copies and are generally arranged in duplicated blocks. Consistent with these data, our analysis revealed that segmental duplication events have played the key role in expanding the soybean PK repertoire and account for the generation of 71.42% of the soybean kinome. Tandem duplications also might have GFT-505 web contributed to the expansion of the soybean kinome but to a much less extent, and their role appears to be restricted to specific subfamilies. It should be noted that subfunctionalization of kinase duplicates and insufficient time for pseudogenization or degeneration may also have contributed to the large size of the soybean PK superfamily. In accordance with this suggestion we found that Ka/Ks values of the syntenically duplicated PKs contributed by the WGD events occurring 59 and 13 Mya were <1, an indication of purifying selection rather than neutral selection for which the Ka/Ks value is expected to be equal to 1. The large numbers of soybean PKs relative to other plant species can be explained mainly by the large numbers of members of a few PK groups. The RLK group in soybean is remarkably large, in that it contains 1418 genes. Similarly, over half of the 2500 PKs in Eucalyptus grandis are RLK members. Previous studies have indicated A global gene co-expression network of soybean PK families The gene expression patterns above pointed to potential coexpression relationships between PK subfamilies. Thus, we constructed the co-expression network of the soybean PK subfamilies using the microarray datasets described above. Construction of the network was performed by determining all pairwise gene expression correlations between PK subfamilies using PCC values and a P value of <0.01. Two independent co-expression networks were generated using tissue and stress response gene expression data. The tissue co-expression network contained 48 nodes and 275 edges separated into one main and six subnetworks. The frequenc