Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination

Abstract

Sexual dimorphism is exhibited in many species across the tree of life with many phenotypic differences mediated by differential expression and alternative splicing of genes present in both sexes. However, the mechanisms that regulate these sex-specific expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, Paternal Genome Elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. P. citri also has no sex chromosomes and as such both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. In this study we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole genome bisulfite sequencing. We have identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifests as more uniform low-levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq we identified extensive sex-specific gene expression and alternative splicing. We found cis-acting DNA methylation is not directly associated with differentially expressed or differentially spliced genes, indicating a broader role for chromosome-wide trans-acting DNA methylation in this species.

DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna

“…Dissecting the interactions between ageing and methylation regulation in Arthropods has lagged by comparison to mammals, although pharmacological inhibition (by RG108) of DNA methyltransferase activity was shown to increase lifespan in honeybees [ 27 ]. DNA methylation has been correlated to phenotypes in several insect orders: it shows sex-specific patterns in the Hemipteran aphids and mealybugs [ 28 , 29 ], nurse and forage caste-specificity in honeybees [ 30 ], and is essential to larval development in the almost negligibly methylated mosquito species Anopheles albimanus [ 31 ]. Despite these correlations, causative links between phenotype and DNA methylation have yet to be established in arthropods [ 7 ].…”

Males That Silence Their Father’s Genes: Genomic Imprinting of a Complete Haploid Genome

“…In mealybugs, spermatogenesis begins at second larval instar ( Nur 1962 ; Bongiorni et al. 2004 ; Bain 2019 ). The reproductive tract consists of a pair of elongated testes—“testes proper”—located at the base of two accessory glands which lead up to the ejaculatory duct ( Nur 1962 ).…”

“…The condensed paternal set is enriched with heterochromatin-associated proteins and histone modifications, such as the H3K9me3-HP1 (heterochromatin protein 1) and H3K27me3-PRC2 (polycomb repressive complex 2) pathways ( Bongiorni et al. 2001 , 2007 ; Bain 2019 ). Interestingly, the maintenance of the heterochromatic state of the paternal genome depends directly on the presence of the maternally inherited set ( Nur 1962 ; Chandra 1963 ; Brown and Nur 1964 ).…”

“…However, it must be noted that male meiosis and the subsequent degradation of spermatids containing paternal chromosomes mostly take place prior to adulthood, during second/third larval instars ( Nur 1962 ; Bongiorni et al. 2004 ; Bain 2019 ). By targeting adult males for RNA-seq, we might have missed paternally expressed genes acting during or just prior to meiosis that could indicate a different scenario.…”

“…Of course, our understanding of the interactions between parental genomes will be incomplete without also characterizing the molecular mechanisms that allow the dynamic spatiotemporal regulation of paternally inherited chromosomes and, ultimately, their germline elimination. The prime candidate in mealybugs is DNA methylation, which differs remarkably between both sexes in P. citri ( Bain et al 2020 ), although current evidence of differential allele-specific methylation in males is contradictory ( Bongiorni et al 1999 ; Buglia et al 1999 ). However, it is unclear how this signal interacts with heterochromatin-associated epigenetic modifications, and whether other players, such as noncoding RNAs, might also play a role.…”