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Lookup NU author(s): Dr Danny Cowan-Turner, Bethan Morris, Dr Osita Nwokeocha, Dr Maxim KapralovORCiD, Emerita Professor Anne Borland
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2024 The Authors. Plants, People, Planet published by John Wiley & Sons Ltd on behalf of New Phytologist Foundation. 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.
Author(s): Cowan-Turner D, Morris BA, Sandehn A, Bernacka-Wojcik I, Stavrinidou E, Powell RF, Leitch IJ, Taylor J, Walker M, Nwokeocha O, Kapralov MV, Borland AM
Publication type: Article
Publication status: Published
Journal: Plants People Planet
Year: 2024
Pages: ePub ahead of Print
Online publication date: 13/05/2024
Acceptance date: 07/04/2024
Date deposited: 29/05/2024
ISSN (electronic): 2572-2611
Publisher: John Wiley and Sons Ltd
URL: https://doi.org/10.1002/ppp3.10517
DOI: 10.1002/ppp3.10517
Data Access Statement: All sequencing data used for the K. blossfeldiana genome assembly and dusk young versus mature K. blossfeldiana RNA-seq were deposited at NCBI under Bio Project number PRJNA915757. The K. blossfeldiana genome assembly has been deposited to https://zenodo.org/record/8188997. A detailed walkthrough of the nuclear genome assembly method is available at Github. (github.com/dcowanturner/Kb_genome).
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