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

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.

A Genome for Edith’s Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes

“…We were able to annotate 23,870 high-quality genes and provide functional information for 20,771 of these. In comparison to another chromosome-scale butterfly genome, we verify that our assembly is not only highly contiguous but accurately assembled as there is high synteny across all of the 31 chromosomes shared between these species ( Hill et al 2019 ; Smolander et al 2022 ). This work provides the foundation upon which detailed study of the eco-evolutionary dynamics of this focal species and its endangered subspecies can now develop.…”

“…We used nucmer (MUMmer4, v.4.0.0beta2) ( Marçais et al 2018 ) to align our final assembly to the chromosome level assembly of the closely related ecological model species, M. cinxia ( Smolander et al 2022 ), with scaffold naming incorporating chromosomal orthology with B. mori and H. melpomene . Synteny was visualized in R with the packages circlize v 0.4.12 ( Gu et al 2014 ) and RColorBrewer v1.1-2, ( Neuwirth and Neuwirth 2014 ), using a set of custom bash and R scripts.…”

Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly

“…The data paves the way for understanding the interplay between molecular mechanisms and micro-evolutionary processes shaping the genome of butterflies in general and provide the first insights into the links between genomic features and the unique lifestyle of this species. The rapid technological advances and dropping costs of DNA-sequencing methods have led to a staggering development rate of high-quality genome assemblies, including many butterfly species (Celorio-Mancera et al, 2021; Gu et al, 2019; Li et al, 2015; Smolander et al, 2022; Yang et al, 2020), and the availability of genomic resources will probably increase almost exponentially in the near future, as a result of the Darwin tree of Life (/https://www.darwintreeoflife.org/), the European Reference Genome Atlas (ERGA; https://www.erga-biodiversity.eu/) and other similar initiatives. However, detailed and curated genome annotation data are more time-consuming and expensive to generate and therefore still limiting comparative/population genomic and genotype-phenotype association approaches, not the least in butterflies (Davey et al, 2017; Hill et al, 2019; Van Belleghem et al, 2017).…”

“…Under-standing how recombination breaks down linkage disequilibrium between physically linked regions is also important for the efficient design of association studies aimed at coupling genetic variation to phenotypic traits. Despite these important contributions to evolutionary genomics research, detailed recombination maps are only available for a handful of butterfly species (Beldade et al, 2009; Celorio-Mancera et al, 2021; Davey et al, 2017; Rosser et al, 2022; Smolander et al, 2022; Tunström et al, 2021). In some cases, link-age maps have been used to improve and/or verify the correctness of physical genome assemblies, but analysis of the recombination rate has not been thoroughly assessed in many butterfly species.…”

The fine-scale recombination rate variation and associations with genomic features in a butterfly

“…Potential associations between recombination and TE densities have mainly been investigated in organisms with defined centromeres (Kent et al 2017), while investigations in holocentric species are scarce (but see Lavoie et al 2013, Baril Hayward 2022, Smolander et al 2022). To investigate the potential asso- ciations between the recombination rate and genomic features in the wood white, we used density information for TEs previously identified in the species (Höök et al 2022).…”