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Morandin C, Brendel VP. Tools and applications for integrative analysis of DNA methylation in social insects. Mol Ecol Resour 2021; 22:1656-1674. [PMID: 34861105 DOI: 10.1111/1755-0998.13566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole-genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analysing several publicly available social insect WGBS data sets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.
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Affiliation(s)
- Claire Morandin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Volker P Brendel
- Departments of Biology and Computer Science, Indiana University, Bloomingto, Indiana, USA
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Huo SM, Zhang YY, Song ZR, Xiong XH, Hong XY. The potential pigmentation-related genes in spider mites revealed by comparative transcriptomes of the red form of Tetranychus urticae. INSECT MOLECULAR BIOLOGY 2021; 30:580-593. [PMID: 34309936 DOI: 10.1111/imb.12727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/27/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Colouration in spider mites is due to the presence of carotenoids with diverse colours, including yellows, oranges and reds. Tetranychus urticae has two main colour forms, red and green. Although a ketolase has been implicated in determining the colour, the underlying genetic basis of body colour divergence between the two forms has remained unclear. Based on a combination of comparative transcriptomes and RNA interference, we found that a gene encoding a cytochrome P450 enzyme of the CYP4 clan (CYP389B1) had remarkably high expression in adult females of the red T. urticae, as well as in hybrids obtained by crossing the red and green forms. Down-regulation of this gene by RNA interference resulted in decreased accumulation of red pigment. Up-regulation of the expressions of a scavenger receptor gene (SCARB1) and a mitochondrial glycine transporter (SLC25A38) also strongly contributed to red colour development in adult females. Suppressing the mRNA levels of these genes also resulted in reduced accumulation of red pigment in the three other spider mites with red body colour. Our results provide evidence that the body colour divergence between the two forms is caused by different expressions of pigmentation-related genes, and point to a possible role of a novel cytochrome P450 gene (CYP389B1) in regulating red-orange body colour. These findings expand the number of candidate cytochrome P450 genes involved in endogenous pigmentation and will help to understand their roles in determining colour patterns in mites and other species.
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Affiliation(s)
- S-M Huo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Y-Y Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Z-R Song
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-H Xiong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Morandin C, Brendel VP, Sundström L, Helanterä H, Mikheyev AS. Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect. Mol Ecol 2019; 28:1975-1993. [PMID: 30809873 DOI: 10.1111/mec.15062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/14/2022]
Abstract
Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversial. Here, we perform well replicated, integrated analyses of DNA methylation and gene expression in brains of an ant (Formica exsecta) with distinct female castes using traditional approaches (tests of differential methylation) combined with a novel approach (analysis of co-expression and co-methylation networks). We found differences in expression and methylation profiles between workers and queens at different life stages, as well as some overlap between DNA methylation and expression at the functional level. Large portions of the transcriptome and methylome are organized into "modules" of genes, some significantly associated with phenotypic traits of castes and developmental stages. Several gene co-expression modules are preserved in co-methylation networks, consistent with possible regulation of caste-specific gene expression by DNA methylation. Surprisingly, brain co-expression modules were highly preserved when compared with a previous study that examined whole-body co-expression patterns in 16 ant species, suggesting that these modules are evolutionarily conserved and for specific functions in various tissues. Altogether, these results suggest that DNA methylation participates in regulation of caste specialization and age-related physiological changes in social insects.
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Affiliation(s)
- Claire Morandin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Åbo, Finland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana.,Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Heikki Helanterä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Ecology and Genetics Research Unit, Faculty of Science, University of Oulu, Oulu, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, Japan.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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