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Journal article
Insights into the Red Seaweed Asparagopsis taxiformis Using an Integrative Multi-Omics Analysis
Plants, Vol.14(10), pp.1-26
2025
PMID: 40431088
Abstract
The red seaweed Asparagopsis taxiformis (Bonnemaisoniaceae, Rhodophyta) produces a bioactive natural product, bromoform, which, when fed to ruminant livestock, can eradicate methane emissions. However, to cultivate enough A. taxiformis to produce a yield that would have a meaningful impact on global greenhouse gas emissions, we need to advance our current understanding of the biology of this seaweed species. Here, we used both a domesticated diploid tetrasporophyte (>1.5 years in culture) and wild samples to establish a high-quality draft nuclear genome for A. taxiformis (lineage 6 based upon phylogenetic analyses using the cox2-3 spacer). The constructed nuclear genome is 142 Mb in size (including 70.67% repeat regions) and was determined to encode for approximately 10,474 protein-coding genes, including those associated with secondary metabolism, photosynthesis, and defence. To obtain information regarding molecular differences between cultured and wild tetrasporophytes, we further explored differential gene expression relating to their different growth environments. Cultured tetrasporophytes, which contained a relatively higher level of bromoform compared to wild tetrasporophytes, demonstrated an enrichment of regulatory factors, such as protein kinases and transcription factors, whereas wild tetrasporophytes were enriched for the expression of defence and stress-related genes. Wild tetrasporophytes also expressed a relatively high level of novel secretory genes encoding proteins with von Willebrand factor A protein domains (named rhodophyte VWAs). Gene expression was further confirmed by proteomic investigation of cultured tetrasporophytes, resulting in the identification of over 400 proteins, including rhodophyte VWAs, and numerous enzymes and phycobiliproteins, which will facilitate future functional characterisation of this species. In summary, as the most comprehensive genomic resource for any Asparagopsis species, this resource for lineage 6 provides a novel avenue for seaweed researchers to interrogate genomic information, which will greatly assist in expediating production of Asparagopsis to meet demand by both aquaculture and agriculture, and to do so with economic and environmental sustainability.
Details
- Title
- Insights into the Red Seaweed Asparagopsis taxiformis Using an Integrative Multi-Omics Analysis
- Authors
- Min Zhao (Corresponding Author) - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringTomas Lang - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringZubaida Patwary - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringAndrew L. Eamens - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringTianfang Wang - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringJessica Webb - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringGiuseppe C. Zuccarello - Victoria University of WellingtonAna Wegner-Thépot - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringCharlotte O’Grady - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringDavid Heyne - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringLachlan McKinnie - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringCecilia Pascelli - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringNori Satoh - Okinawa Institute of Science and Technology Graduate UniversityEiichi Shoguchi - Okinawa Institute of Science and Technology Graduate UniversityAlexandra H. Campbell - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringNicholas A. Paul - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringScott F. Cummins (Corresponding Author) - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
- Publication details
- Plants, Vol.14(10), pp.1-26
- Publisher
- MDPI AG
- Date published
- 2025
- DOI
- 10.3390/plants14101523
- ISSN
- 2223-7747
- PMID
- 40431088
- Copyright note
- © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
- Data Availability
- Raw data of all genome sequencing was submitted to NCBI BioProject and SRA database under a BioProject accession number PRJNA809757. Phylogenetic identification data was submitted under GenBank accession number OP779373. Mass spectrometry peptide raw data was deposited into the PRIDE database under accession number PXD035669. The genome assembly can also be accessed via University of the Sunshine Coast at https://doi.org/10.25907/00708.
- Organisation Unit
- School of Health - Biomedicine; Cancer Research Cluster; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 991129985502621
- Output Type
- Journal article
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