The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Abstract

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

Figure 1. Number of proteins in different classes of orthologous groups.

The statistics for M. cinxia are very similar to those for other Lepidoptera, including 5,977 conserved core proteins, 7,177 taxonomic order-, family- or species-specific proteins and 3,513 proteins without detectable sequence similarity to others. There appears to be rapid turnover of gene content in the genomes, indicated by the large proportion of order- and family-specific groups, which represent either rapidly evolving genes or dispensable ancient paralogues that have been deleted from most other lineages. Species codes are as used in SwissProt: Melci=Melitaea cinxia, Helme=Heliconius melpomene, Danpl=Danaus plexippus, Bommo=Bombyx mori, Pluxy=Plutella xylostella, Dromo=Drosophila mojavensis, Drosi=Drosophila simulans, Drome=Drosophila melanogaster, Culqu=Culex quinquefasciatus, Anoga=Anopheles gambiae, Aedae=Aedes aegypti, Apime=Apis mellifera, Harsa=Harpegnathos saltator, Solin=Solenopsis invicta, Nasvi=Nasonia vitripennis, Trica=Tribolium castaneum, Acypi=Acyrthosiphon pisum, Pedhu=Pediculus humanus, Dappu=Daphnia pulex, Ixosc=Ixodes scapularis, Felca=Felis catus and Ratno=Rattus norvegicus. The lepidopteran species are highlighted with a box. See Supplementary Note 8 for the definition of classes.

Figure 2. Chromosome mapping of Melitaea cinxia to Bombyx mori and Heliconius melpomene.

(a) One-to-one orthologues (4,485) connecting M. cinxia and B. mori chromosomes and (b) 3,869 one-to-one orthologues connecting M. cinxia and H. melpomene chromosomes. M. cinxia chromosomes are numbered according to chromosome length from the largest to the smallest. The links leading from M. cinxia chromosomes are pooled into bins that are ordered within chromosomes. Bands drawn in M. cinxia chromosomes represent bin borders. Chromosome 1 is the Z chromosome in M. cinxia and B. mori. The fusion chromosomes are shaded with blue and the orthologous chromosomes in M. cinxia with red.

Figure 3. Haploid chromosome numbers mapped onto the lepidopteran tree of life and a phylogenetic hypothesis for Nymphalidae.

(a) The lepidopteran tree of life showing the placement of focal species with their haploid chromosome number (n). The named species are those for which whole-genome sequence and linkage map are available (only linkage map for Biston). Major clades, often defined as superfamilies, are coloured. In the Papilionoidea clade (the butterflies), the family Nymphalidae is highlighted in light blue, with the putative ancestral chromosome number of n=31 (for justification see panel b). The topology is taken from Regier et al. (b) Haploid chromosome number mapped onto a phylogenetic hypothesis for Nymphalidae. The character state ‘31’ is shown to be the most likely ancestral state for the family. The four species with whole-genome sequences are highlighted. Details of the source of phylogenetic hypothesis as well as chromosome numbers are found in the Supplementary Note 11.

Figure 4. The chronogram of the lepidopteran species for which the whole-genome sequence or linkage map, or both, are available together with haploid chromosome numbers.

Times of divergence for Danaus, Heliconius and Melitaea are taken from Wahlberg et al., the other times of divergence are from Wahlberg et al..

Figure 5. Melitaea cinxia chromosomes involved in fusion events in Bombyx mori and Heliconius melpomene.

(a) Fusions unique to H. melpomene. (b) Fusions in which the same M. cinxia orthologous chromosomes have been fused in both B. mori and H. melpomene. Each box represents one superscaffold in M. cinxia and a scaffold in H. melpomene. The colour of each box is derived from the chromosomal origin of the orthologous segment in the M. cinxia genome (compare with Supplementary Fig. 36). Horizontal lines within the boxes show the corresponding loci in M. cinxia chromosomes, and red vertical lines show recombination sites (bin boundaries) in the linkage map.

Figure 6. Relationships among chromosome length, chromosome rearrangement rate and percentage of repetitive elements in the 31 chromosomes of Melitaea cinxia.

The rearrangement rate is described by the number of chromosomal breakpoints scaled by the number of orthologues. A plane minimizing squared error was fitted to the data and is shown in grey. Drop lines are drawn from each point to this plane.