Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

BACKGROUND: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with...

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Autores principales: Smolander, Olli-Pekka, Blande, Daniel, Ahola, Virpi, Rastas, Pasi, Tanskanen, Jaakko, Kammonen, Juhana I, Oostra, Vicencio, Pellegrini, Lorenzo, Ikonen, Suvi, Dallas, Tad, DiLeo, Michelle F, Duplouy, Anne, Duru, Ilhan Cem, Halimaa, Pauliina, Kahilainen, Aapo, Kuwar, Suyog S, Kärenlampi, Sirpa O, Lafuente, Elvira, Luo, Shiqi, Makkonen, Jenny, Nair, Abhilash, de la Paz Celorio-Mancera, Maria, Pennanen, Ville, Ruokolainen, Annukka, Sundell, Tarja, Tervahauta, Arja I, Twort, Victoria, van Bergen, Erik, Österman-Udd, Janina, Paulin, Lars, Frilander, Mikko J, Auvinen, Petri, Saastamoinen, Marjo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Data Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756199/
https://www.ncbi.nlm.nih.gov/pubmed/35022701
http://dx.doi.org/10.1093/gigascience/giab097
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author Smolander, Olli-Pekka
Blande, Daniel
Ahola, Virpi
Rastas, Pasi
Tanskanen, Jaakko
Kammonen, Juhana I
Oostra, Vicencio
Pellegrini, Lorenzo
Ikonen, Suvi
Dallas, Tad
DiLeo, Michelle F
Duplouy, Anne
Duru, Ilhan Cem
Halimaa, Pauliina
Kahilainen, Aapo
Kuwar, Suyog S
Kärenlampi, Sirpa O
Lafuente, Elvira
Luo, Shiqi
Makkonen, Jenny
Nair, Abhilash
de la Paz Celorio-Mancera, Maria
Pennanen, Ville
Ruokolainen, Annukka
Sundell, Tarja
Tervahauta, Arja I
Twort, Victoria
van Bergen, Erik
Österman-Udd, Janina
Paulin, Lars
Frilander, Mikko J
Auvinen, Petri
Saastamoinen, Marjo
author_facet Smolander, Olli-Pekka
Blande, Daniel
Ahola, Virpi
Rastas, Pasi
Tanskanen, Jaakko
Kammonen, Juhana I
Oostra, Vicencio
Pellegrini, Lorenzo
Ikonen, Suvi
Dallas, Tad
DiLeo, Michelle F
Duplouy, Anne
Duru, Ilhan Cem
Halimaa, Pauliina
Kahilainen, Aapo
Kuwar, Suyog S
Kärenlampi, Sirpa O
Lafuente, Elvira
Luo, Shiqi
Makkonen, Jenny
Nair, Abhilash
de la Paz Celorio-Mancera, Maria
Pennanen, Ville
Ruokolainen, Annukka
Sundell, Tarja
Tervahauta, Arja I
Twort, Victoria
van Bergen, Erik
Österman-Udd, Janina
Paulin, Lars
Frilander, Mikko J
Auvinen, Petri
Saastamoinen, Marjo
author_sort Smolander, Olli-Pekka
collection PubMed
description BACKGROUND: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. RESULTS: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. CONCLUSIONS: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.
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spelling pubmed-87561992022-01-13 Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map Smolander, Olli-Pekka Blande, Daniel Ahola, Virpi Rastas, Pasi Tanskanen, Jaakko Kammonen, Juhana I Oostra, Vicencio Pellegrini, Lorenzo Ikonen, Suvi Dallas, Tad DiLeo, Michelle F Duplouy, Anne Duru, Ilhan Cem Halimaa, Pauliina Kahilainen, Aapo Kuwar, Suyog S Kärenlampi, Sirpa O Lafuente, Elvira Luo, Shiqi Makkonen, Jenny Nair, Abhilash de la Paz Celorio-Mancera, Maria Pennanen, Ville Ruokolainen, Annukka Sundell, Tarja Tervahauta, Arja I Twort, Victoria van Bergen, Erik Österman-Udd, Janina Paulin, Lars Frilander, Mikko J Auvinen, Petri Saastamoinen, Marjo Gigascience Data Note BACKGROUND: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. RESULTS: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. CONCLUSIONS: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species. Oxford University Press 2022-01-12 /pmc/articles/PMC8756199/ /pubmed/35022701 http://dx.doi.org/10.1093/gigascience/giab097 Text en © The Author(s) 2022. Published by Oxford University Press GigaScience. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Smolander, Olli-Pekka
Blande, Daniel
Ahola, Virpi
Rastas, Pasi
Tanskanen, Jaakko
Kammonen, Juhana I
Oostra, Vicencio
Pellegrini, Lorenzo
Ikonen, Suvi
Dallas, Tad
DiLeo, Michelle F
Duplouy, Anne
Duru, Ilhan Cem
Halimaa, Pauliina
Kahilainen, Aapo
Kuwar, Suyog S
Kärenlampi, Sirpa O
Lafuente, Elvira
Luo, Shiqi
Makkonen, Jenny
Nair, Abhilash
de la Paz Celorio-Mancera, Maria
Pennanen, Ville
Ruokolainen, Annukka
Sundell, Tarja
Tervahauta, Arja I
Twort, Victoria
van Bergen, Erik
Österman-Udd, Janina
Paulin, Lars
Frilander, Mikko J
Auvinen, Petri
Saastamoinen, Marjo
Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title_full Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title_fullStr Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title_full_unstemmed Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title_short Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
title_sort improved chromosome-level genome assembly of the glanville fritillary butterfly (melitaea cinxia) integrating pacific biosciences long reads and a high-density linkage map
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756199/
https://www.ncbi.nlm.nih.gov/pubmed/35022701
http://dx.doi.org/10.1093/gigascience/giab097
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