Neo-sex chromosome characterization and its applications to studies of chromosomal evolution
Alignment of the draft neo-Y scaffolds to the neo-X revealed the approximate boundary between the ancestral-autosomal and ancestral-X portions of the neo-X chromosome. Our data suggest that the ancestral-X region may be slightly larger than 10 Mb (Fig. 5), or approximately 14% of the total length of the neo-X chromosome.
Using linkage mapping and genome assemblies, we found that markers in each of the first four principal components (PCs) identified in Trevoy et al. (2019) were physically linked to three chromosomes. These findings validate the use of PC loadings exhibiting marker plateaus to infer genomic linkage in the absence of a linkage map or chromosome-scale genome assembly. Trevoy et al. (2019) also showed that high PC 2 loadings distinguished SNPs in beetles that were almost entirely heterozygous in males and homozygous in females. They hypothesized that this reflects sex-specific nucleotide changes in paralogous neo-X linked versus neo-Y linked genes. If true, the male-specific heterozygosity found by Trevoy et al. (2019) actually resulted from erroneous alignment of neo-Y reads to the ancestral-autosomal region of the neo-X. Support for this conclusion comes from neo-Y scaffold locations on the draft genome, as identified by Dowle et al. (2017), mapping to our neo-X chromosome (Fig. 5). Further, if any of the draft genome scaffolds containing high-loading SNPs on the PC 2 axis identified by Trevoy et al. (2019) truly represented the male copy of the neo-X, we would expect some of them to align to the ancestral-X region as well, but this was not the case. Rather, we identify a mosaic-like pattern across neo-Y scaffolds that is consistent with both the recent origin of mountain pine beetle neo-sex chromosomes and the gradual accumulation of chromosome-specific mutations.
Karyotype varies across Dendroctonus and includes both typical Xyp sex chromosomes (as found for the majority of beetles) and neo-sex chromosomes (Zúñiga et al., 2002), like in mountain pine beetle. We have generated the first chromosome-level assembly in this genus, and others are forthcoming (Casola et al., 2020; Keeling et al., 2020). The mountain pine beetle neo-sex chromosomes represent approximately 30% of its genome content. Genome assemblies from the other Dendroctonus spp. should identify which ancestral autosomes became part of the neo-sex chromosomes in mountain pine beetle, and the consequences of such large sex chromosomes for mountain pine beetle physiology and ecology.
This improved mountain pine beetle genome may provide another window for studying chromosome evolution relating to neo-XY development and Y chromosome degeneration. Currently, much of our understanding of neo-XY systems comes from studies of Drosophila spp. (Wei & Bachtrog, 2019), while mammalian and Drosophila systems provide insight into Y degeneration (e.g., Muller’s ratchet) (Charlesworth & Charlesworth, 2000). However, neither mammals nor Drosophila are ideal systems for these studies because divergence times among species can be considerable – their Y chromosomes tend to be quite old, exhibiting substantial degeneration (Charlesworth & Charlesworth, 2000). Thus, evolutionarily more recent neo-Y systems, like that of mountain pine beetle, are particularly valuable.
Several other features of the mountain pine beetle genome, coupled with the improved genomic resource presented here, make it an interesting chromosomal evolution study system. First, compared to traditional chiasmatic or achiasmatic XY systems, the ancestral Xypkaryotypes of many Dendroctonus spp. may more readily result in neo-XY systems. (Blackmon & Demuth, 2014; Dutrillaux & Dutrillaux, 2017). Second, Y turnover, due to degeneration followed by neo-Y gains, is common in many beetle groups, and is approximately 34% inDendroctonus (Blackmon & Demuth, 2014). Third, neo-Y haplotype groups corresponding to geography and low hybrid viability have been identified in the mountain pine beetle (Dowle et al., 2017). Thus, further study of the mountain pine beetle genome may allow us to answer a variety of questions relating to Muller’s ratchet-related concepts, and implications for neo-Y chromosome turnover, in phylogeographic and cyclic population irruption contexts.
In conclusion, we completed proximity ligation-based scaffolding of the draft genome of D. ponderosae , supported by linkage mapping, to generate chromosome-level assemblies. These assemblies support genome-level investigations of many biological processes for this keystone species and silvicultural pest and will serve as a valuable resource for functional and evolutionary studies of otherDendroctonus species, other Scolytinae and Coleoptera more generally.