Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C3, CAM comparative tool

• Published in: Plants, people, planet Vol. 6; no. 6; pp. 1314 - 1328
• Main Authors: 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.
• Format: Journal Article
• Language: English
• Published: Lancaster John Wiley & Sons, Inc 01-11-2024; Wiley
• Subjects: Abiotic stress; Abscisic acid; abscisic acid signalling; Acids; age inducible Crassulacean acid metabolism; Assembly; Crassulacean acid metabolism; Crassulacean acid metabolism (CAM); Drought; drought stress; Flowers & plants; Gene expression; Gene sequencing; Genera; Genomes; genomics; Haplotypes; Humidity; Metabolism; Metabolites; Nanopore sequencings; Nucleotide sequence; Ornamental plants; Photosynthesis; Physiology; Plant layout; Plant species; Plants (botany); Ploidy; Scaffolding; Species; Species diversity; Tetraploidy; Transcriptomes; transcriptomics
• ISSN: 2572-2611; 2572-2611
• DOI: 10.1002/ppp3.10517

Societal Impact Statement
Research efforts in plant biology have often been focused on sequenced and well‐studied ‘model’ organisms. Despite the advent of relatively inexpensive genome sequencing, most plant taxonomic groups are underrepresented, with few species that ‘represent’ the diversity of whole genera. This study describes an economical guide to sequencing a non‐model organism, which may be useful in reducing the cost of sequencing more species within genera and across plant life. This method was used to develop Kalanchoë blossfeldiana as a resource for comparing C3 and the water‐conserving mode of photosynthesis known as Crassulacean acid metabolism (CAM) within the same plant.
Summary
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 Kalanchoë 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.
The 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.
Research efforts in plant biology have often been focused on sequenced and well‐studied ‘model’ organisms. Despite the advent of relatively inexpensive genome sequencing, most plant taxonomic groups are underrepresented, with few species that ‘represent’ the diversity of whole genera. This study describes an economical guide to sequencing a non‐model organism, which may be useful in reducing the cost of sequencing more species within genera and across plant life. This method was used to develop Kalanchoë blossfeldiana as a resource for comparing C3 and the water‐conserving mode of photosynthesis known as Crassulacean acid metabolism (CAM) within the same plant.