Advancing responsible genomic analyses of ancient mollusc shells.

Autor: Martin-Roy R; Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France., Thyrring J; Department of Ecoscience, Aarhus University, Aarhus, Denmark.; Arctic Research Centre, Aarhus University, Aarhus, Denmark., Mata X; Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France., Bangsgaard P; Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark., Bennike O; Geological Survey of Denmark and Greenland, Copenhagen, Denmark., Christiansen G; Museum of Copenhagen, Copenhagen, Denmark., Funder S; Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark., Gotfredsen AB; Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark., Gregersen KM; Natural History Museum of Denmark, Copenhagen, Denmark., Hansen CH; Museum of Copenhagen, Copenhagen, Denmark., Ilsøe PC; Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark., Klassen L; Museum Østjylland, Randers, Denmark., Kristensen IK; Museum Salling, Skive, Denmark., Ravnholt GB; Museum of Copenhagen, Copenhagen, Denmark., Marin F; Biogéosciences, UMR6282, CNRS-EPHE-uB, University of Burgundy, EPHE, Dijon, France., Der Sarkissian C; Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2024 May 06; Vol. 19 (5), pp. e0302646. Date of Electronic Publication: 2024 May 06 (Print Publication: 2024).
DOI: 10.1371/journal.pone.0302646
Abstrakt: The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Martin-Roy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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