A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird
Abstract Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arc...
Published in: | Genome Biology and Evolution |
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Oxford University Press (OUP)
2023
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Online Access: | http://dx.doi.org/10.1093/gbe/evad153 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evad153/51141873/evad153.pdf https://academic.oup.com/gbe/article-pdf/15/8/evad153/51267264/evad153.pdf |
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croxfordunivpr:10.1093/gbe/evad153 2023-10-01T03:53:55+02:00 A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird Sozzoni, Marcella Ferrer Obiol, Joan Formenti, Giulio Tigano, Anna Paris, Josephine R Balacco, Jennifer R Jain, Nivesh Tilley, Tatiana Collins, Joanna Sims, Ying Wood, Jonathan Benowitz-Fredericks, Z Morgan Field, Kenneth A Seyoum, Eyuel Gatt, Marie Claire Léandri-Breton, Don-Jean Nakajima, Chinatsu Whelan, Shannon Gianfranceschi, Luca Hatch, Scott A Elliott, Kyle H Shoji, Akiko Cecere, Jacopo G Jarvis, Erich D Pilastro, Andrea Rubolini, Diego Katz, Laura 2023 http://dx.doi.org/10.1093/gbe/evad153 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evad153/51141873/evad153.pdf https://academic.oup.com/gbe/article-pdf/15/8/evad153/51267264/evad153.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ Genome Biology and Evolution volume 15, issue 8 ISSN 1759-6653 Genetics Ecology, Evolution, Behavior and Systematics journal-article 2023 croxfordunivpr https://doi.org/10.1093/gbe/evad153 2023-09-01T10:54:47Z Abstract Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic, and temperate zones, suffered a steep population decline following an abrupt warming of sea surface temperature across its distribution range and is currently listed as Vulnerable by the International Union for the Conservation of Nature. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level reference genome and annotation for the black-legged kittiwake using a combination of Pacific Biosciences HiFi sequencing, Bionano optical maps, Hi-C reads, and RNA-Seq data. The final assembly spans 1.35 Gb across 32 chromosomes, with a scaffold N50 of 88.21 Mb and a BUSCO completeness of 97.4%. This genome assembly substantially improves the quality of a previous draft genome, showing an approximately 5× increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the diversification of Charadriiformes. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype–genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems. Article in Journal/Newspaper Arctic Black-legged Kittiwake rissa tridactyla Subarctic Oxford University Press (via Crossref) Arctic Pacific Genome Biology and Evolution 15 8 |
institution |
Open Polar |
collection |
Oxford University Press (via Crossref) |
op_collection_id |
croxfordunivpr |
language |
English |
topic |
Genetics Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Ecology, Evolution, Behavior and Systematics Sozzoni, Marcella Ferrer Obiol, Joan Formenti, Giulio Tigano, Anna Paris, Josephine R Balacco, Jennifer R Jain, Nivesh Tilley, Tatiana Collins, Joanna Sims, Ying Wood, Jonathan Benowitz-Fredericks, Z Morgan Field, Kenneth A Seyoum, Eyuel Gatt, Marie Claire Léandri-Breton, Don-Jean Nakajima, Chinatsu Whelan, Shannon Gianfranceschi, Luca Hatch, Scott A Elliott, Kyle H Shoji, Akiko Cecere, Jacopo G Jarvis, Erich D Pilastro, Andrea Rubolini, Diego A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
topic_facet |
Genetics Ecology, Evolution, Behavior and Systematics |
description |
Abstract Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic, and temperate zones, suffered a steep population decline following an abrupt warming of sea surface temperature across its distribution range and is currently listed as Vulnerable by the International Union for the Conservation of Nature. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level reference genome and annotation for the black-legged kittiwake using a combination of Pacific Biosciences HiFi sequencing, Bionano optical maps, Hi-C reads, and RNA-Seq data. The final assembly spans 1.35 Gb across 32 chromosomes, with a scaffold N50 of 88.21 Mb and a BUSCO completeness of 97.4%. This genome assembly substantially improves the quality of a previous draft genome, showing an approximately 5× increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the diversification of Charadriiformes. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype–genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems. |
author2 |
Katz, Laura |
format |
Article in Journal/Newspaper |
author |
Sozzoni, Marcella Ferrer Obiol, Joan Formenti, Giulio Tigano, Anna Paris, Josephine R Balacco, Jennifer R Jain, Nivesh Tilley, Tatiana Collins, Joanna Sims, Ying Wood, Jonathan Benowitz-Fredericks, Z Morgan Field, Kenneth A Seyoum, Eyuel Gatt, Marie Claire Léandri-Breton, Don-Jean Nakajima, Chinatsu Whelan, Shannon Gianfranceschi, Luca Hatch, Scott A Elliott, Kyle H Shoji, Akiko Cecere, Jacopo G Jarvis, Erich D Pilastro, Andrea Rubolini, Diego |
author_facet |
Sozzoni, Marcella Ferrer Obiol, Joan Formenti, Giulio Tigano, Anna Paris, Josephine R Balacco, Jennifer R Jain, Nivesh Tilley, Tatiana Collins, Joanna Sims, Ying Wood, Jonathan Benowitz-Fredericks, Z Morgan Field, Kenneth A Seyoum, Eyuel Gatt, Marie Claire Léandri-Breton, Don-Jean Nakajima, Chinatsu Whelan, Shannon Gianfranceschi, Luca Hatch, Scott A Elliott, Kyle H Shoji, Akiko Cecere, Jacopo G Jarvis, Erich D Pilastro, Andrea Rubolini, Diego |
author_sort |
Sozzoni, Marcella |
title |
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
title_short |
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
title_full |
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
title_fullStr |
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
title_full_unstemmed |
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake ( Rissa tridactyla ), a Declining Circumpolar Seabird |
title_sort |
chromosome-level reference genome for the black-legged kittiwake ( rissa tridactyla ), a declining circumpolar seabird |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1093/gbe/evad153 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evad153/51141873/evad153.pdf https://academic.oup.com/gbe/article-pdf/15/8/evad153/51267264/evad153.pdf |
geographic |
Arctic Pacific |
geographic_facet |
Arctic Pacific |
genre |
Arctic Black-legged Kittiwake rissa tridactyla Subarctic |
genre_facet |
Arctic Black-legged Kittiwake rissa tridactyla Subarctic |
op_source |
Genome Biology and Evolution volume 15, issue 8 ISSN 1759-6653 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/gbe/evad153 |
container_title |
Genome Biology and Evolution |
container_volume |
15 |
container_issue |
8 |
_version_ |
1778521003634196480 |