1. Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C3, CAM comparative tool
- Author
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Cowan-Turner, Daniel, Morris, Bethan A., Sandéhn, Alexandra, Bernacka Wojcik, Iwona, Stavrinidou, Eleni, Powell, Robyn F., Leitch, Ilia J., Taylor, Jessica, Walker, Max, Nwokeocha, Osita, Kapralov, Maxim V., Borland, Anne M., Cowan-Turner, Daniel, Morris, Bethan A., Sandéhn, Alexandra, Bernacka Wojcik, Iwona, Stavrinidou, Eleni, Powell, Robyn F., Leitch, Ilia J., Taylor, Jessica, Walker, Max, Nwokeocha, Osita, Kapralov, Maxim V., and Borland, Anne M.
- Abstract
Despite the increasing number of well-studied plant species with well-annotated genomes across plant life, there are few densely sampled genera with more than a couple of genome sequences representing the diversity of whole genera. Here, we develop an economic approach to full-genome sequencing that could be used to sequence many species within a genus. We made use of the Nanopore rapid sequencing kit to assist in plant genome assembly, dramatically reducing the cost. Here we applied this method to cost-effectively develop genomic resources for Kalancho & euml; blossfeldiana, a commercially important ornamental, in which Crassulacean Acid Metabolism (CAM), a water-conserving mode of photosynthesis can be induced. We present a physiological and biochemical characterisation of Kalanchoe blossfeldiana with its nuclear and chloroplastic genome and a comparative C3, CAM dusk transcriptome. We apply this approach to a complex tetraploid genome, making use of a relative species for chromosomal scaffolding to reduce assembly ploidy, we provide a resource for future gene expression studies. We highlight its limitations, e.g. the need for deeper sequencing to accurately resolve genome structure and haplotypes without using a relative species for scaffolding. T he study demonstrates the merits of K. blossfeldiana as a comparative system for studying C3 and CAM within a plant and has identified substantial changes in the dusk transcriptome between young C3 and mature CAM K. blossfeldiana leaves in response to age-induced CAM, and shows that in the absence of abiotic stress, CAM induction still involves the engagement of drought and abscisic acid (ABA) response pathways., Funding Agencies|Biotechnology and Biological Sciences Research Council (BBSRC); [2132439]; [2462247]
- Published
- 2024
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