The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

Abstract

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders? We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta. We find that synteny largely scales with clade age, with younger clades, such as Lepidoptera, having especially high synteny. However, we do find subtle differences in the maintenance of synteny and its rate of decay among the insect orders.

How the Easter Egg Weevils Got Their Spots: Phylogenomics reveals Müllerian Mimicry inPachyrhynchus(Coleoptera, Curculionidae)

“…More analyses are required to compare the design of Tagliacollo and Lanfear 2018 63 to the design we propose here to make a decisive decision of which scheme is optimal for UCE partitioning. The partition method we employ is the only one that accommodates the combination of neighboring or co-genic UCEs 51 In summation, we clearly demonstrated that many of the mimetic color patterns observed in sympatry are due to convergent evolution and not simply due to inheritance. Based on our observations in natural history collections, we hypothesize that convergence between these independent color pattern forms is likely driven by frequency dependent selection.…”

“…Identifying UCE loci within genomic windows: We used methodologies that are similar to Van Dam et al 2020 51 for combining UCE loci. First, we identified UCE loci that are within 25 kb non-overlapping windows, as similar window sizes were used in Edelman et al 2019 59 .…”

“…More analyses are required to compare the design of Tagliacollo and Lanfear 2018 63 to the design we propose here to make a decisive decision of which scheme is optimal for UCE partitioning. The partition method we employ is the only one that accommodates the combination of neighboring or co-genic UCEs 51 (the method of Tagliacollo and Lanfear 2018 63 could be easily updated). The asymmetry in variation away from the UCE core is perhaps due to the way in which UCE loci are treated in the alignment process, mainly that difficult to align regions are trimmed in a less symmetric manner around the core of the locus.…”

How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).

“…Identifying UCE loci within genomic windows: We used methodologies that are similar to Van Dam et al 2020 51 for combining UCE loci. First, we identified UCE loci that are within 25 kb non-overlapping windows, as similar window sizes were used in Edelman et al 2019 59 .…”

“…using the "deleteEmptyCells" function, followed by removing any ragged ends of the matrix with the "trimEnds" function, with a minimum of four taxa present in the alignment. Below we expand on partitioning procedures to consider the potential site rate heterogeneity found in UCE loci as well as partition loci found in the same genomic window or potentially the same gene 51 . We use an alternative partitioning scheme from Van Dam et al 2017 and Tagliacollo and Lanfear 2018 62,63 .…”