Kaikai Zhu, Hui Liu, Xinlu Chen, Qunkang Cheng and Zong-Ming (Max) Cheng

BMC Plant Biology 2018  18:199

Background

Crassulacean acid metabolism (CAM) plants use water 20–80% more efficiently by shifting stomata opening and primary CO₂ uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biological process. However, few PKs have been functionally analyzed precisely due to their abundance and potential functional redundancy (caused by numerous gene duplications).

Results

In this study, we systematically identified a total of 758 predicted PK genes in the genome of a CAM plant, pineapple (Ananas comosus). The pineapple kinome was classified into 20 groups and 116 families based on the kinase domain sequences. The RLK was the largest group, containing 480 members, and over half of them were predicted to locate at the plasma membrane. Both segmental and tandem duplications make important contributions to the expansion of pineapple kinome based on the synteny analysis. Ka/Ks ratios showed all of the duplication events were under purifying selection. The global expression analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal expression patterns. Forty PK genes in a cluster performed higher expression levels in green leaf tip than in white leaf base, and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base tissues.

Conclusions

Our findings provide insights into the evolution and biological function of pineapple PKs and a foundation for further functional analysis of PKs in CAM plants. The gene duplication, expression, and coexpression analysis helped us to rapidly identify the key candidates in pineapple kinome, which may play roles in the carbon fixation process in pineapple and help engineering CAM pathway into C3 crops for improved drought tolerance.

See: https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-018-1389-z

Figure 1: Classification and phylogenetic analysis of pineapple PK families. The maximum-likelihood tree was constructed by amino acid sequences of the kinase domain using the FastTree. Branches were colored to represent two different groups. The non-RLK groups are marked with green branch; the RLK group is marked with red branch. The detailed phylogeny was provided in Additional file 2: Figure S1