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Höglund J, Dias G, Olsen RA, Soares A, Bunikis I, Talla V, Backström N. A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern. Genome Biol Evol 2024; 16:evae031. [PMID: 38368625 PMCID: PMC10901555 DOI: 10.1093/gbe/evae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024] Open
Abstract
The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.
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Affiliation(s)
- Jacob Höglund
- Animal Ecology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Guilherme Dias
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna 17165, Sweden
| | - André Soares
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 752 37, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
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Mora P, Hospodářská M, Voleníková AC, Koutecký P, Štundlová J, Dalíková M, Walters JR, Nguyen P. Sex-biased gene content is associated with sex chromosome turnover in Danaini butterflies. Mol Ecol 2024:e17256. [PMID: 38180347 DOI: 10.1111/mec.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.
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Affiliation(s)
- Pablo Mora
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Monika Hospodářská
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Petr Koutecký
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jana Štundlová
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - James R Walters
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Shipilina D, Näsvall K, Höök L, Vila R, Talavera G, Backström N. Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly. Genomics 2022; 114:110481. [PMID: 36115505 DOI: 10.1016/j.ygeno.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/14/2023]
Abstract
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden; Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236 Uppsala, Sweden.
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Roger Vila
- The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Martim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS. A genome for Edith's checkerspot butterfly: an insect with complex host-adaptive suites and rapid evolutionary responses to environmental changes. Genome Biol Evol 2022; 14:6649524. [PMID: 35876165 PMCID: PMC9348621 DOI: 10.1093/gbe/evac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 11/15/2022] Open
Abstract
Insects have been key players in the assessments of biodiversity impacts of anthropogenically driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith’s Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting these dynamics over several decades. However, studies of the underlying genetic bases of these responses have been hampered by missing genomic resources, limiting the ability to connect genomic responses to environmental change. Using a combination of Oxford Nanopore long reads, haplotype merging, HiC scaffolding followed by Illumina polishing, we generated a highly contiguous and complete assembly (contigs n = 142, N50 = 21.2 Mb, total length = 607.8 Mb; BUSCOs n = 5,286, single copy complete = 97.8%, duplicated = 0.9%, fragmented = 0.3%, missing = 1.0%). A total of 98% of the assembled genome was placed into 31 chromosomes, which displayed large-scale synteny with other well-characterized lepidopteran genomes. The E. editha genome, annotation, and functional descriptions now fill a missing gap for one of the leading field-based ecological model systems in North America.
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Affiliation(s)
- Kalle Tunstrom
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Camille Parmesan
- Station d'Écologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200 Moulis, France.,Biological and Marine Sciences, University of Plymouth, Plymouth, U.K.,Department of Geological Sciences, University of Texas at Austin, U.S.A
| | - Michael C Singer
- Station d'Écologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200 Moulis, France.,Biological and Marine Sciences, University of Plymouth, Plymouth, U.K
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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