High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

Abstract

Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.

Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements

“…We used Swedish (n = 6 families; 186 offspring) and Catalan (n = 6 families; 186 offspring) full-sib families of L. sinapis to develop RAD-seq based linkage maps for two populations that represent the most extreme karyotype variants in the species. Details about family structure, RADseq data generation and preprocessing are available in [21]. To get recombination rate information, the linkage map markers were anchored on recently established chromosome-level assemblies for each respective population [21].…”

“…It should be noted that fission / fusion polymorphisms are known to be segregating in the populations [21] and that the linkage maps used here are composite maps of different families which may add some uncertainty to the estimates of recombination rates. To further investigate the extent of potential individual differences in recombination rate as a consequence of karyotype variation between families within a specific population, we would need to produce individual recombination maps for males homozygous for each karyotype.…”

“…(https://github.com/FelixKrueger/TrimGalore), a wrapper for cutadapt 3.1 [59]. Trimmed reads were mapped to the genome assemblies for each respective population [21] using bwa mem [53]. Variant calling was performed using GATK 4.2.0.0 [60].…”

Lepidopteran Synteny Units (LSUs) reveal deep conservation of macrosynteny in butterflies and moths

“…In terms of future applications, LSUs are easily derived from BUSCO analysis of lepidopteran target genomes and are a simple means to describe the architecture of lepidopteran genomes and their chromosomal evolution. The more complex karyotypes of some lycaenid (blue butterflies) (Lukhtanov 2015) or pierid (white) butterflies (Šíchová et al 2016, Höög et al 2023) are obvious targets for further analysis. BUSCO analysis with LSUs also offers another practical use: to quickly determine places of interest like breakpoints in chromosomal rearrangements for a subsequent detailed analysis of the nature of such breakpoints or fusion points at the nucleotide level.…”

“…Here we develop a homology-based technique for exploring conserved synteny in the butterflies and moths. The Lepidoptera have previously been shown to have wide-ranging synteny or macrosynteny across autosomes and Z chromosomes via a range of different mapping techniques including comparative linkage mapping (Pringle et al 2007; Beldade et al 2009; Baxter et al 2011; Van’t Hof et al 2013), BAC-FISH mapping (Yasukochi et al 2009; Yoshido et al 2011; Sahara et al 2013) by a comparison of annotated long-read sequences (d’Alençon et al2010; The Heliconius Genome Consortium 2012), and by whole-genome comparison (Höök et al 2023, Pazhenkova and Lukhtanov 2023).…”