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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 and Dallas, Tad , et al. (2022) In GigaScience 11.
Abstract

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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
genome, Glanville fritillary, Melitaea cinxia, spatial ecology
in
GigaScience
volume
11
article number
giab097
publisher
Oxford University Press
external identifiers
  • scopus:85123566142
  • pmid:35022701
ISSN
2047-217X
DOI
10.1093/gigascience/giab097
language
English
LU publication?
yes
id
44ab7865-4c9d-405f-acb1-0fe274fd23b5
date added to LUP
2022-04-11 12:09:51
date last changed
2024-06-15 10:20:21
@article{44ab7865-4c9d-405f-acb1-0fe274fd23b5,
  abstract     = {{<p>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.</p>}},
  author       = {{Smolander, Olli Pekka and Blande, Daniel and Ahola, Virpi and Rastas, Pasi and Tanskanen, Jaakko and Kammonen, Juhana I. and Oostra, Vicencio and Pellegrini, Lorenzo and Ikonen, Suvi and Dallas, Tad and Dileo, Michelle F. and Duplouy, Anne and Duru, Ilhan Cem and Halimaa, Pauliina and Kahilainen, Aapo and Kuwar, Suyog S. and Kärenlampi, Sirpa O. and Lafuente, Elvira and Luo, Shiqi and Makkonen, Jenny and Nair, Abhilash and De La Paz Celorio-Mancera, Maria and Pennanen, Ville and Ruokolainen, Annukka and Sundell, Tarja and Tervahauta, Arja I. and Twort, Victoria and Van Bergen, Erik and Österman-Udd, Janina and Paulin, Lars and Frilander, Mikko J. and Auvinen, Petri and Saastamoinen, Marjo}},
  issn         = {{2047-217X}},
  keywords     = {{genome; Glanville fritillary; Melitaea cinxia; spatial ecology}},
  language     = {{eng}},
  publisher    = {{Oxford University Press}},
  series       = {{GigaScience}},
  title        = {{Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map}},
  url          = {{http://dx.doi.org/10.1093/gigascience/giab097}},
  doi          = {{10.1093/gigascience/giab097}},
  volume       = {{11}},
  year         = {{2022}},
}