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Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C3, CAM comparative tool
Newcastle Univ, England; Australian Natl Univ, Australia.
Newcastle Univ, England.
Linköpings universitet, Institutionen för teknik och naturvetenskap, Laboratoriet för organisk elektronik. Linköpings universitet, Tekniska fakulteten.ORCID-id: 0009-0004-1403-1868
Linköpings universitet, Institutionen för teknik och naturvetenskap, Laboratoriet för organisk elektronik. Linköpings universitet, Tekniska fakulteten.
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2024 (Engelska)Ingår i: Plants, People, Planet, E-ISSN 2572-2611Artikel i tidskrift (Refereegranskat) Epub ahead of print
Abstract [en]

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.

Ort, förlag, år, upplaga, sidor
WILEY , 2024.
Nyckelord [en]
abscisic acid signalling; age inducible Crassulacean acid metabolism; Crassulacean acid metabolism (CAM); drought stress; genomics; Nanopore sequencings; transcriptomics
Nationell ämneskategori
Biologisk systematik
Identifikatorer
URN: urn:nbn:se:liu:diva-203748DOI: 10.1002/ppp3.10517ISI: 001221269100001OAI: oai:DiVA.org:liu-203748DiVA, id: diva2:1861394
Anmärkning

Funding Agencies|Biotechnology and Biological Sciences Research Council (BBSRC); [2132439]; [2462247]

Tillgänglig från: 2024-05-28 Skapad: 2024-05-28 Senast uppdaterad: 2024-05-28

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Sandéhn, AlexandraBernacka Wojcik, IwonaStavrinidou, Eleni
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Laboratoriet för organisk elektronikTekniska fakulteten
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Plants, People, Planet
Biologisk systematik

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