They constitute their own cluster only distantly related to the rest of the family

rhizobial signalling molecules playing a fundamental role in the initiation of nitrogenfixing symbiosis in legumes. LCOs are perceived by several receptors in host roots and initiate a cascade of signalling events leading to the formation of root nodules. While the pronounced response of soybean PKs to LCOs is in agreement with the well-documented effects of LCOs on plant development and morphogenesis as well as biotic and abiotic stress PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19812251 responses, it provides the foundation to speculate that PK genes may have been co-opted to regulate a wide range of biological functions including symbiotic interactions. In addition to the RLK/Pelle family, the soybean kinome contains a significant percentage of CAMKs with 70 genes coding for calcium-dependent PKs. The expansion of this family may reflect an adaptive evolution that allows soybean plants to perceive different calcium signals that mediate the plant response to environmental stress. On the other hand, several PK subfamilies have been subjected to limited expansion in soybean and remained low in copy number. These subfamilies probably represent ancient families in which new members have not been retained because they did not confer a selective advantage over the ancestral copy. Alternatively, these subfamilies may be involved in more basic and less environmentdependent cellular processes where the driving forces behind continuous expansion and evolution are very limited. Domain organization and intron/exon arrangement have frequently been used as a supporting indication for evolutionary relationships among genes and species. Domain organization analysis revealed that 74 PK genes contained two or three kinase domains. Because many PKs are known to form homo- and heterodimers, the twoand three- kinase domain structure of soybean PKs may be functionally equivalent to dimerized PKs where cooperative activity of two or three kinase domains may be required for specific substrates. Functional studies of truncated variants of these PKs will provide valuable insights into their mechanism of regulation and substrate specificity. The gene structure of the PK subfamilies clearly elucidated their differential propensity to lose or acquire introns. We found that the proportion of intronless PK genes was much less than that of total intronless genes in the soybean genome, suggesting that intron gain has significantly contributed to the structural divergence of the soybean PK superfamily. It seems likely that the structural evolution of soybean PKs is conditioned by similar mechanisms controlling intron gain and loss in both monocot and eudicot species because the patterns of intron number distribution are very similar. We observed that intron/exon position and arrangement patterns were tightly conserved in a number of subfamilies, specifically those whose expansion had been contributed by the WGD occurring 13 Mya, consistent with their close evolutionary relationship. In contrast, other members of subfamilies displayed a high structural diversity but a strong conservation of the kinase domain. This may reflect gene family expansion from old paralogues or multiple ancestral origins of the gene family. Finally, the wide structure differences of the PK supergene family DHMEQ web associated with functional divergence may have contributed significantly to the high retention of the duplicate genes in soybean. In conclusion, our analyses of soybean PKs revealed their wide expansion, and extensive divergence in gene stru