Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species
Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the patte...
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ftnerc:oai:nora.nerc.ac.uk:533758 2023-05-15T17:33:32+02:00 Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species Vendrami, David L.J. Hoffman, Joseph I. Wilding, Craig S. 2022-12-21 text http://nora.nerc.ac.uk/id/eprint/533758/ https://nora.nerc.ac.uk/id/eprint/533758/1/genes-14-00014.pdf https://www.mdpi.com/2073-4425/14/1/14 en eng MDPI https://nora.nerc.ac.uk/id/eprint/533758/1/genes-14-00014.pdf Vendrami, David L.J.; Hoffman, Joseph I. orcid:0000-0001-5895-8949 Wilding, Craig S. 2022 Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species [in special issue: Genomics in Aquaculture and Fisheries] Genes, 14 (1), 14. 18, pp. https://doi.org/10.3390/genes14010014 <https://doi.org/10.3390/genes14010014> cc_by_4 CC-BY Publication - Article PeerReviewed 2022 ftnerc https://doi.org/10.3390/genes14010014 2023-02-10T00:01:46Z Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus. Article in Journal/Newspaper North Atlantic Natural Environment Research Council: NERC Open Research Archive Genes 14 1 14 |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
English |
description |
Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus. |
format |
Article in Journal/Newspaper |
author |
Vendrami, David L.J. Hoffman, Joseph I. Wilding, Craig S. |
spellingShingle |
Vendrami, David L.J. Hoffman, Joseph I. Wilding, Craig S. Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
author_facet |
Vendrami, David L.J. Hoffman, Joseph I. Wilding, Craig S. |
author_sort |
Vendrami, David L.J. |
title |
Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
title_short |
Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
title_full |
Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
title_fullStr |
Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
title_full_unstemmed |
Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species |
title_sort |
heterogeneous genomic divergence landscape in two commercially important european scallop species |
publisher |
MDPI |
publishDate |
2022 |
url |
http://nora.nerc.ac.uk/id/eprint/533758/ https://nora.nerc.ac.uk/id/eprint/533758/1/genes-14-00014.pdf https://www.mdpi.com/2073-4425/14/1/14 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
https://nora.nerc.ac.uk/id/eprint/533758/1/genes-14-00014.pdf Vendrami, David L.J.; Hoffman, Joseph I. orcid:0000-0001-5895-8949 Wilding, Craig S. 2022 Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species [in special issue: Genomics in Aquaculture and Fisheries] Genes, 14 (1), 14. 18, pp. https://doi.org/10.3390/genes14010014 <https://doi.org/10.3390/genes14010014> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3390/genes14010014 |
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Genes |
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14 |
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14 |
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