De novo Transcriptome Assembly and Comparison of C ₃, C ₃-C ₄, and C ₄ Species of Tribe Salsoleae (Chenopodiaceae)

C ₄ photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C ₄ from ancestral C ₃ photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C ₃ and C ₄ species have significantly increased our understanding of C ₄ functioning and evolution. In Chenopodiaceae, a family that is rich in C ₄ origins and photosynthetic types, the anatomy, physiology and phylogeny of C ₄, C ₂, and C ₃ species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. mRNA from assimilating organs of each species was sequenced in triplicates, and sequence reads were de novo assembled. These novel genetic resources were then analyzed to provide a better understanding of differential gene expression between C ₃, C ₂ and C ₄ species. All three analyzed C ₄ species belong to the NADP-ME type as most genes encoding core enzymes of this C ₄ cycle are highly expressed. The abundance of photorespiratory transcripts is decreased compared to the C ₃ and C ₂ species. Like in other C ₄ lineages of Caryophyllales, our results suggest that PEPC1 is the C ₄-specific isoform in Salsoleae. Two recently identified transporters from the PHT4 protein family may not only be related to the C ₄ syndrome, but also active in C ₂ photosynthesis in Salsoleae. In the two populations of the C ₂ species S. divaricata transcript abundance of several C ₄ genes are slightly increased, however, a C ₄ cycle is not detectable in the carbon isotope values. Most of the core enzymes of photorespiration are highly increased in the C ₂ species compared to both C ₃ and C ₄ species, confirming a successful establishment of the C ₂ photosynthetic pathway. Furthermore, a function of PEP-CK in C ₂ photosynthesis appears likely, since PEP-CK gene expression is not only increased in S. divaricata but also in C ₂ species of other groups.