Abstract
BackgroundEven though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood. Epigenomic profiles may represent key factors, with unknown contributions to the development of multiple phenotypes, and social-insect castes are a good model for elucidation of the underlying mechanisms. Nonetheless, previous studies have failed to identify genes associated with aberrant gene expression and methylation profiles because of the lack of suitable methodology that can address this problem properly.MethodsA recently proposed principal component analysis (PCA)-based and tensor decomposition (TD)-based unsupervised feature extraction (FE) can solve this problem because these two approaches can deal with gene expression and methylation profiles even when a small number of samples is available.ResultsPCA-based and TD-based unsupervised FE methods were applied to the analysis of gene expression and methylation profiles in the brains of two social insects, Polistes canadensis and Dinoponera quadriceps. Genes associated with differential expression and methylation between castes were identified, and analysis of enrichment of Gene Ontology terms confirmed reliability of the obtained sets of genes from the biological standpoint.ConclusionsBiologically relevant genes, shown to be associated with significant differential gene expression and methylation between castes, were identified here for the first time. The identification of these genes may help understand the mechanisms underlying epigenetic control of development of multiple phenotypes under the same genomic conditions.
Highlights
Even though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood
The methylation profile principal component analysis (PCA)-based unsupervised feature extraction (FE) was applied to the methylation profiles of P. canadensis and D. quadriceps
Patalano et al [8] did not find genes associated with the emergence of distinct methylation patterns between queens and workers, but the results presented in Fig. 3(a) and (c) show minor differences between queens and workers, suggesting that the selected genes may have different methylation profiles between queens and workers overall
Summary
Even though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood. Juvenile and adult organisms have different sizes or must survive in distinct environments, and these conditions require different phenotypes. More striking examples are castes of social insects, such as ants and bees, which can form two distinct forms: queens and workers, both female [1]. They are usually closely related, but queens and workers have different sizes and lifespans. The mechanism that potentially allows social insects to form castes with distinct body plans is the epigenome [2, 3], which is flexible and can lead to the formation of different phenotypes without genomic alterations. It is important to determine the correlation between an epigenome and phenotype by analyzing gene expression
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