title: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species.
abstract: C(4) photosynthesis outperforms the ancestral C(3) state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C(3) backgrounds. However, the genetic architecture of C(4) photosynthesis remains largely unknown. To define the divergence in gene expression modules between C(3) and C(4) photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C(4)) and Tarenaya hassleriana (C(3)), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C(3) and C(4) species. We found that known C(4) genes were recruited to photosynthesis from different expression domains in C(3), including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C(3) root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C(4) bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C(4) leaf.
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Canan
authors.initials: C
authors.lastname: Külahoglu
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Alisandra K
authors.initials: AK
authors.lastname: Denton
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Sommer
authors.affiliation: Institute of Informatics, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Janina
authors.initials: J
authors.lastname: Maß
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Schliesky
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Wrobel
authors.affiliation: Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Berckmans
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Elsa
authors.initials: E
authors.lastname: Gongora-Castillo
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Simon
authors.affiliation: Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.
authors.forename: Lieven
authors.initials: L
authors.lastname: De Veylder
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bräutigam
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany andreas.weber@uni-duesseldorf.de.
authors.forename: Andreas P M
authors.initials: AP
authors.lastname: Weber
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D019684:Magnoliopsida / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome