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Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism
Author(s) -
Heyduk Karolina,
Ray Jeremy N.,
Ayyampalayam Saravanaraj,
LeebensMack James
Publication year - 2018
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.1002/ajb2.1017
Subject(s) - biology , crassulacean acid metabolism , gene , phylogenetics , phylogenetic tree , gene expression , transcriptome , gene co expression network , genetics , context (archaeology) , evolutionary biology , botany , photosynthesis , paleontology , gene ontology
Premise of the Study The relative ease of high throughput sequencing is facilitating comprehensive phylogenomic and gene expression studies, even for nonmodel groups. To date, however, these two approaches have not been merged; while phylogenomic methods might use transcriptome sequences to resolve relationships, assessment of gene expression patterns in a phylogenetic context is less common. Here we analyzed both carbon assimilation and gene expression patterns of closely related species within the Agavoideae (Asparagaceae) to elucidate changes in gene expression across weak and strong phenotypes for Crassulacean acid metabolism ( CAM ). Methods Gene expression patterns were compared across four genera: Agave ( CAM ), which is paraphyletic with Polianthes (weak CAM ) and Manfreda ( CAM ), and Beschorneria (weak CAM ). RNA ‐sequencing was paired with measures of gas exchange and titratable acidity. Climate niche space was compared across the four lineages to examine abiotic factors and their correlation to CAM . Key Results Expression of homologous genes showed both shared and variable patterns in weak and strong CAM species. Network analysis highlights that despite shared expression patterns, highly connected genes differ between weak and strong CAM , implicating shifts in regulatory gene function as key for the evolution of CAM . Variation in carbohydrate metabolism between weak and strong CAM supports the importance of sugar turnovers for CAM physiology. Conclusions Integration of phylogenetics and RNA ‐sequencing provides a powerful tool to study the evolution of CAM photosynthesis across closely related but photosynthetically variable species. Our findings regarding shared or shifted gene expression and regulation of CAM via carbohydrate metabolism have important implications for efforts to engineer the CAM pathway into C 3 food and biofuel crops.