Comparative sequencing of closely related C3 and C4 species
Project contact: Julian Hibbard, University of Cambridge
The aim is to generate comprehensive transcriptomes from closely related C3 and C4 species. C4 photosynthesis is used by the most productive crops and native vegetation on the planet. The pathway is therefore of significant interest to research that aim to increase productivity of food (e.g. the international C4 rice project, http://c4rice.irri.org) and biofuels (e.g. the use of Switchgrass, which is the C4 species Panicum virgatum L.; see http://bioenergy.ornl.gov/papers/misc/switgrs.html), as well as to scientists working on productivity of native vegetation. Because the pathway represents one of the most remarkable examples of convergent evolution so far documented, it is also of significant interest to evolutionary biologists.
The C4 pathway involves alterations to leaf development, cell biology and biochemistry, but despite this complexity it has evolved at least 45 times independently within the angiosperms. Defining the extent to which separate lineages of C4 plants have repeatedly recruited the same proteins and mechanisms is dependent on having deep sequence information for closely related C3 and C4 lineages. Genome sequences are available for the C4 monocotyledons Zea mays, and this can be compared to Oryza sativa (C3). JGI is currently sequencing additional monocotyledonous C4 plants such as Sorghum bicolor and Setaria italica. However, the evolution of C4 in the grasses is polyphyletic, and so more comprehensive sequence information is required for this group. To gain real insight into the evolution of C4 photosynthesis in this clade that contains the majority of the worlds’ most important crops, we will generate deep sequence information for additional members of this critical group.
In addition, for other lineages of C4 plants, and significantly, for C4 dicotyledons there is little available sequence information. The aim is therefore to dramatically increase sequence coverage for closely related C3 and C4 grasses, and also to provide equivalent information for key groups within the major lineages of dicotyledons that have evolved C4 photosynthesis.
To gain significant insights into the convergent evolution of the C4 pathway we propose the following: each species is subjected to a single round of transcriptome sequencing from cDNA generated from mature leaves. This will generate high coverage of genes that are associated with the pathway, and comparison between species will determine the extent to which the pathway itself is convergent. Con-generic pairs of C3 and C4 species will be used where possible.