Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam
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Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam Abigail Ramsøe 1,2 & Melody S. Clark 3 & Victoria A. Sleight 3,4,5 Received: 9 January 2020 / Revised: 27 April 2020 / Accepted: 4 May 2020 # The Author(s) 2020
Abstract A computationally predicted gene regulatory network (GRN), generated from mantle-specific gene expression profiles in the Antarctic clam Laternula elliptica, was interrogated to test the regulation and interaction of duplicated inducible hsp70 paralogues. hsp70A and hsp70B were identified in the GRN with each paralogue falling into unique submodules that were linked together by a single shared second neighbour. Annotations associated with the clusters in each submodule suggested that hsp70A primarily shares regulatory relationships with genes encoding ribosomal proteins, where it may have a role in protecting the ribosome under stress. hsp70B, on the other hand, interacted with a suite of genes involved in signalling pathways, including four transcription factors, cellular response to stress and the cytoskeleton. Given the contrasting submodules and associated annotations of the two hsp70 paralogues, the GRN analysis suggests that each gene is carrying out additional separate functions, as well as being involved in the traditional chaperone heat stress response, and therefore supports the hypothesis that subfunctionalization has occurred after gene duplication. The GRN was specifically produced from experiments investigating biomineralization; however, this study shows the utility of such data for investigating multiple questions concerning gene duplications, interactions and putative functions in a non-model species. Keywords Heat stress . Hypoxia . Gene duplication . Ribosome . Signalling . Cytoskeleton
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12192-020-01118-9) contains supplementary material, which is available to authorized users. * Melody S. Clark [email protected] * Victoria A. Sleight [email protected] 1
BioArCh, Department of Archaeology, University of York, York YO1 7EP, UK
2
Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
3
British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
4
Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
5
Present address: School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
Improvement in the understanding of the genomic content of any non-model species is impeded by the lack of functional annotation. Annotation rates, particularly in environmental invertebrates, are often low, and many genes assembled within an experimentally derived transcriptome are either designated as unknown or require more detailed analysis to extract conservation at the domain level. Annotation can be particularly problematical when attempting to differentia
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