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

Olli-Pekka Smolander; Daniel Blande; Virpi Ahola; Pasi Rastas; Jaakko Tanskanen; Juhana I Kammonen; Vicencio Oostra; Lorenzo Pellegrini; Suvi Ikonen; Tad Dallas; Michelle F DiLeo; Anne Duplouy; Ilhan Cem Duru; Pauliina Halimaa; Aapo Kahilainen; Suyog S Kuwar; Sirpa O Kärenlampi; Elvira Lafuente; Shiqi Luo; Jenny Makkonen; Abhilash Nair; Maria de la Paz Celorio-Mancera; Ville Pennanen; Annukka Ruokolainen; Tarja Sundell; Arja I Tervahauta; Victoria Twort; Erik van Bergen; Janina Österman-Udd; Lars Paulin; Mikko J Frilander; Petri Auvinen; Marjo Saastamoinen

doi:10.1093/gigascience/giab097

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

Gigascience. 2022 Jan 12;11(1):giab097. doi: 10.1093/gigascience/giab097.

Authors

Olli-Pekka Smolander^{1

2}, Daniel Blande³, Virpi Ahola^{3

4}, Pasi Rastas¹, Jaakko Tanskanen⁵, Juhana I Kammonen¹, Vicencio Oostra^{3

6}, Lorenzo Pellegrini¹, Suvi Ikonen³, Tad Dallas⁷, Michelle F DiLeo³, Anne Duplouy^{3

8}, Ilhan Cem Duru¹, Pauliina Halimaa⁹, Aapo Kahilainen³, Suyog S Kuwar^{10

11}, Sirpa O Kärenlampi⁹, Elvira Lafuente¹², Shiqi Luo¹³, Jenny Makkonen⁹, Abhilash Nair³, Maria de la Paz Celorio-Mancera¹⁴, Ville Pennanen¹⁵, Annukka Ruokolainen³, Tarja Sundell¹, Arja I Tervahauta⁹, Victoria Twort⁸, Erik van Bergen³, Janina Österman-Udd³, Lars Paulin¹, Mikko J Frilander¹, Petri Auvinen¹, Marjo Saastamoinen^{3

16}

Affiliations

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

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.

Keywords: Melitaea cinxia; Glanville fritillary; genome; spatial ecology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Butterflies* / genetics
Chromosome Mapping
Chromosomes / genetics
Fritillaria* / genetics
Genome
Male