Cleome transcriptome comparison
RNA-seq of two species of Cleome provides insight into the evolution of C4 photosynthesis
To gain insight into the extent to which gene expression is altered in C4 compared to C3 leaves, and to provide a platform to identify candidate genes involved in incompletely understood processes associated with C4 photosynthesis, we have carried out a comparative digital gene expression analysis on the transcriptomes of leaves from closely related C3 and C4 species, using RNA-seq. Digital gene expression analysis is based on the random generation of sequence tags that are proportional to the abundance of the corresponding transcripts in a particular sample. Pyrosequencing has previously been shown to be useful in defining transcriptomes of sequenced as well as incompletely sequenced plant species and here we show that it can be used for differential analysis of gene expression of related species. For our analysis, we used C3 and C4 members of Cleome, a genus that contains the most closely related C4 species to Arabidopsis thaliana. The rationale for using Cleome in this approach was that its phylogenetic proximity to A. thaliana should facilitate annotation and interpretation of sequence data obtained. In addition, Cleome gynandra represents the first dicotyledonous C4 species, and member of the NAD-Malic Enzyme (NAD-ME) sub-type of C4 photosynthesis for which a comprehensive and quantitative transcriptome dataset is available.
To provide insight into the extent to which gene expression is altered between C3 and C4 species, and to identify candidates underlying the alterations in a C4 leaf compared to C3 leaf we have used RNA-seq of closely related C3 and C4 species from the genus Cleome. We show that this approach can be used to gain insight into the evolution of complex traits that differ between species.