Improved chromosome-level genome assembly of the Glanville fritillary butterfly (<i>Melitaea cinxia</i>) integrating Pacific Biosciences long reads and a high-density linkage map-Reference-Cited by-同舟云学术

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

Published:2022 Issue: Volume:11 Page:
ISSN:2047-217X
Container-title:GigaScience
language:en
Short-container-title:

Author:

Smolander Olli-Pekka¹²^ORCID,Blande Daniel³^ORCID,Ahola Virpi³⁴^ORCID,Rastas Pasi¹^ORCID,Tanskanen Jaakko⁵,Kammonen Juhana I¹^ORCID,Oostra Vicencio³⁶^ORCID,Pellegrini Lorenzo¹^ORCID,Ikonen Suvi³,Dallas Tad⁷^ORCID,DiLeo Michelle F³^ORCID,Duplouy Anne³⁸^ORCID,Duru Ilhan Cem¹^ORCID,Halimaa Pauliina⁹,Kahilainen Aapo³^ORCID,Kuwar Suyog S¹⁰¹¹^ORCID,Kärenlampi Sirpa O⁹,Lafuente Elvira¹²^ORCID,Luo Shiqi¹³^ORCID,Makkonen Jenny⁹^ORCID,Nair Abhilash³^ORCID,de la Paz Celorio-Mancera Maria¹⁴^ORCID,Pennanen Ville¹⁵^ORCID,Ruokolainen Annukka³,Sundell Tarja¹,Tervahauta Arja I⁹^ORCID,Twort Victoria⁸^ORCID,van Bergen Erik³^ORCID,Österman-Udd Janina³^ORCID,Paulin Lars¹^ORCID,Frilander Mikko J¹^ORCID,Auvinen Petri¹^ORCID,Saastamoinen Marjo³¹⁶^ORCID

Affiliation:

1. Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland

2. Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia

3. Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland

4. Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, 171 77 Stockholm, Hong Kong

5. Natural Resource Institute (LUKE), 00790 Helsinki, Finland

6. Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool CH64 7TE, UK

7. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA

8. Department of Biology, Lund University, 223 62 Lund, Sweden

9. Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 KUOPIO, Finland

10. Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611-0620, USA

11. Department of Zoology, Loknete Vyankatrao Hiray Arts, Science & Commerce College, 422003, Maharashtra, India

12. Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland

13. College of Plant Protection, China Agricultural University, Beijing 100083, China

14. Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden

15. Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland

16. Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland

Abstract

AbstractBackgroundThe 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.ResultsThe 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.ConclusionsThe genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.

Funder

European Research Council

Academy of Finland

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

Link

https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giab097/42276835/giab097.pdf

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