Fig 1.
Pachyrhynchus sulphureomaculatus, lateral habitus.
(photo by A. Cabras). Hi-C contact map heatmap of Pachyrhynchus sulphureomaculatus Schultze, 1922. Eleven chromosome boundaries are indicated by black lines. Heatmap scale lower left, range in counts of mapped Hi-C reads per megabase squared. Rabl-like pattern (grouping of telomeres and centromeres to the nuclear envelope) highlighted along chromosome 1, top row, top of open triangles point to contact between centromere regions, arrows indicate centromere to centromere contact between chromosomes 1 and 2. X-like pattern between adjacent off diagonal regions indicative of contact between distal portions of chromosomes.
Table 1.
Summary statistics for final assembly.
Table 2.
Summary statistics for final assembly by chromosome.
Fig 2.
Histogram of repeat content for weevil genomes examined.
Subfamily classification appears below the histograms. Latin names are in italic font with common names below in parentheses. Genome size largely corresponds to repeat content.
Fig 3.
Heat map of gene density and non-repetitive DNA per 1 Mb sliding window.
The 11 chromosomes are in the same order as in the Hi-C heat map (Fig 1) and fasta file of the genome. Repetitive content higher towards the distal portions of the chromosomes.
Table 3.
Results from genome annotation, lengths in bp.
Fig 4.
Chronogram and ideograms of 7 beetle genomes which have chromosome level assemblies.
Chromosomes largely remain intact with few translocations relative to reshuffling within a chromosome. Colors correspond to the 11 chromosomes of Pachyrhynchus sulphureomaculatus, top row of ideogram plots. Each line represents a BUSCO gene connecting its position on the chromosome of P. sulphureomaculatus (top row, respectively) to its position on another species (lower row, respectively).
Fig 5.
Stacked bar plots and chromosome mappings of BUSCO genes’ placements.
The Y-axis represents the counts of BUSCO genes from Pachyrhynchus sulphureomaculatus found on the corresponding chromosomes of another species. Colors correspond to P. sulphureomaculatus chromosomes. The numbering scheme (on X-axis) of chromosomes matches the names found in the genome’s fasta file. While most chromosomes are primarily composed of one or two chromosomes, relative to P. sulphureomaculatus, the placement of the BUSCO genes are interleaved in many instances, indicating that while translocations are rare events reshuffling within a chromosome happens much more frequently.
Fig 6.
Pachyrhynchus sulphureomaculatus chromosome 11 and matching homologous chromosomes from taxa samples across the Coleoptera.
Top row, approximate position of Pachyrhynchus chromosome 11 centromere marked with black line, position derived from Hi-C contact map (see Fig 1). Colored lines correspond to the position of BUSCO genes. Blue colors correspond to one chromosome arm and red colors the other. While the majority of BUSCO genes found in Pachyrhynchus chromosome 11 are retained in the other species there is extensive reshuffling in their positions.
Fig 7.
Insecta, gene order conservation score (GOC) of BUSCO genes.
Left, phylogeny of taxa in analyses, derived from BUSCO genes (610,189 AA sites), reconstructed via RAxML-ng, branches colored by insect order. Right, heat map from pairwise comparisons among insects with chromosome level genomes (only genes localized to chromosomes considers in analyses). Comparisons of gene order which are more syntenic (higher GOC scores) appear in yellow boxes, dark purple indicate less synteny between taxa pairs.
Fig 8.
Relationship between synteny and phylogenetic distance across different insect orders.
Lines show the best-fitting exponential decay model. Note the log-transformed y-axis. Phylogenetic distance is calculated from a total tree height of 1. Higher values of the GOC score indicate more synteny, lower values less synteny. Synteny decay rate of Lepidoptera differs substantially, however other insect orders also have distinct rates.