Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Nathan J. Kenny (), Warren R. Francis, Ramón E. Rivera-Vicéns, Ksenia Juravel, Alex de Mendoza, Cristina Díez-Vives, Ryan Lister, Luis A. Bezares-Calderón, Lauren Grombacher, Maša Roller, Lael D. Barlow, Sara Camilli, Joseph F. Ryan, Gert Wörheide, April L. Hill, Ana Riesgo and Sally P. Leys ()
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Nathan J. Kenny: The Natural History Museum
Warren R. Francis: University of Southern Denmark
Ramón E. Rivera-Vicéns: Ludwig-Maximilians-Universität München
Ksenia Juravel: Ludwig-Maximilians-Universität München
Alex de Mendoza: The University of Western Australia
Cristina Díez-Vives: The Natural History Museum
Ryan Lister: The University of Western Australia
Luis A. Bezares-Calderón: University of Exeter
Lauren Grombacher: University of Alberta
Maša Roller: European Bioinformatics Institute
Lael D. Barlow: University of Alberta
Sara Camilli: Bates College
Joseph F. Ryan: University of Florida
Gert Wörheide: Ludwig-Maximilians-Universität München
April L. Hill: Bates College
Ana Riesgo: The Natural History Museum
Sally P. Leys: University of Alberta

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.

Date: 2020
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DOI: 10.1038/s41467-020-17397-w

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