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.

Keywords: Chromosome fissions/fusions; Genome rearrangements; Karyotype evolution; Lepidoptera; Linkage map.

Fig. 1

Comparison of synteny between the Leptidea species and the two references B. mori and M. cinxia. The karyotype of the latter species is assumed to represent the ancestral lepidopteran karyotype (Ahola et al., 2014). Chromosomes are ordered by size in each species. Pairwise comparisons between B. mori and each respective Leptidea lineage are available in Supplementary figure 10

Fig. 2

Estimated number of chromosomal rearrangement events in the different Leptidea species/populations. Fusions are highlighted in red and fissions in blue. Numbers show total counts for each branch and shared events are shown in parentheses. Divergence times are based on Talla et al. (2017).

Fig. 3

Fusion polymorphisms in Swedish L. sinapis and respective homologous regions in the other Leptidea species and populations. Lines show individual alignments (> 90% similarity) and colors represent homologous regions. Chromosomes have been rotated to enhance visualization. Note that chromosomes 26 and 27 are not homologous to the chromosome with the same number in the opposite sex in Swedish L. sinapis. Ast, Asturias population; Cat, Catalan population

Fig. 4

Linkage groups for (a) Catalan L. sinapis families and (b) Swedish families. Colors represent specific chromosomes in the male genome assembly for the Swedish (n = 26–28) and Catalan (n = 51–53) L. sinapis populations, respectively

Fig. 5

Composition of sequence elements in (A) fusion and (B) fission breakpoints as compared to the rest of the genomes for L. reali and L. sinapis (the outgroup L. juvernica was excluded from the analysis). Comparisons were performed separately for when the species were used as references or queries. The histograms show distributions of element densities generated by 100 k iterations of random genomic sampling with replacement. Vertical lines show mean density of elements in breakpoints, highlighted in red if significant and black if non-significant. FDR-adjusted p-values are indicated for significant tests. All p-values, means, and standard deviations are reported in Supplementary table 7. CDS, coding sequence; LINE, long interspersed elements; SINE, short interspersed elements; LTR, long terminal repeats; DNA, DNA transposons; RC, rolling-circle TEs