Comparative genomics and signatures of selection in North Atlantic eels
Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic lev...
Published in: | Marine Genomics |
---|---|
Main Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2022
|
Subjects: | |
Online Access: | https://hdl.handle.net/11585/900889 https://doi.org/10.1016/j.margen.2022.100933 https://www.sciencedirect.com/science/article/pii/S1874778722000113 |
id |
ftunibolognairis:oai:cris.unibo.it:11585/900889 |
---|---|
record_format |
openpolar |
spelling |
ftunibolognairis:oai:cris.unibo.it:11585/900889 2024-04-14T08:00:58+00:00 Comparative genomics and signatures of selection in North Atlantic eels Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca 2022 ELETTRONICO https://hdl.handle.net/11585/900889 https://doi.org/10.1016/j.margen.2022.100933 https://www.sciencedirect.com/science/article/pii/S1874778722000113 eng eng info:eu-repo/semantics/altIdentifier/pmid/35182837 info:eu-repo/semantics/altIdentifier/wos/WOS:000766634600001 volume:62 firstpage:1 lastpage:11 numberofpages:11 journal:MARINE GENOMICS https://hdl.handle.net/11585/900889 doi:10.1016/j.margen.2022.100933 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85124587235 https://www.sciencedirect.com/science/article/pii/S1874778722000113 info:eu-repo/semantics/openAccess Anguilla anguilla Anguilla rostrata F(ST) Selection XP-EHH iHS Animal Atlantic Ocean Human Polymorphism Single Nucleotide Anguilla Genomics info:eu-repo/semantics/article 2022 ftunibolognairis https://doi.org/10.1016/j.margen.2022.100933 2024-03-21T16:47:40Z Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the F-ST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events. Article in Journal/Newspaper Anguilla anguilla European eel North Atlantic IRIS Università degli Studi di Bologna (CRIS - Current Research Information System) Marine Genomics 62 100933 |
institution |
Open Polar |
collection |
IRIS Università degli Studi di Bologna (CRIS - Current Research Information System) |
op_collection_id |
ftunibolognairis |
language |
English |
topic |
Anguilla anguilla Anguilla rostrata F(ST) Selection XP-EHH iHS Animal Atlantic Ocean Human Polymorphism Single Nucleotide Anguilla Genomics |
spellingShingle |
Anguilla anguilla Anguilla rostrata F(ST) Selection XP-EHH iHS Animal Atlantic Ocean Human Polymorphism Single Nucleotide Anguilla Genomics Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca Comparative genomics and signatures of selection in North Atlantic eels |
topic_facet |
Anguilla anguilla Anguilla rostrata F(ST) Selection XP-EHH iHS Animal Atlantic Ocean Human Polymorphism Single Nucleotide Anguilla Genomics |
description |
Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the F-ST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events. |
author2 |
Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca |
format |
Article in Journal/Newspaper |
author |
Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca |
author_facet |
Pujolar, Jose Martin Jacobsen, Magnus Wulff Bertolini, Francesca |
author_sort |
Pujolar, Jose Martin |
title |
Comparative genomics and signatures of selection in North Atlantic eels |
title_short |
Comparative genomics and signatures of selection in North Atlantic eels |
title_full |
Comparative genomics and signatures of selection in North Atlantic eels |
title_fullStr |
Comparative genomics and signatures of selection in North Atlantic eels |
title_full_unstemmed |
Comparative genomics and signatures of selection in North Atlantic eels |
title_sort |
comparative genomics and signatures of selection in north atlantic eels |
publishDate |
2022 |
url |
https://hdl.handle.net/11585/900889 https://doi.org/10.1016/j.margen.2022.100933 https://www.sciencedirect.com/science/article/pii/S1874778722000113 |
genre |
Anguilla anguilla European eel North Atlantic |
genre_facet |
Anguilla anguilla European eel North Atlantic |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/35182837 info:eu-repo/semantics/altIdentifier/wos/WOS:000766634600001 volume:62 firstpage:1 lastpage:11 numberofpages:11 journal:MARINE GENOMICS https://hdl.handle.net/11585/900889 doi:10.1016/j.margen.2022.100933 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85124587235 https://www.sciencedirect.com/science/article/pii/S1874778722000113 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1016/j.margen.2022.100933 |
container_title |
Marine Genomics |
container_volume |
62 |
container_start_page |
100933 |
_version_ |
1796305670359744512 |