ORCID Profile
0000-0002-0811-901X
Current Organisation
University of Helsinki
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Publisher: Cold Spring Harbor Laboratory
Date: 19-08-2021
DOI: 10.1101/2021.08.19.457008
Abstract: DNA methylation is a common epigenetic signaling tool and an important biological process which is widely studied in a large array of species. The presence, level, and function of DNA methylation varies greatly across species. In insects, DNA methylation systems are reduced, and methylation rates are often low. Low methylation levels probed by whole genome bisulfite 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-analyzing several publicly available social insect WGBS data sets, comprising 70 s les 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. DNA methylation in the honeybee genome occurs almost entirely at CpG sites. Methylation rates are small compared to rates in mammalian or plant genomes. De novo analysis of all published honeybee methylation studies and statistical modeling suggests that the CpG methylome consists of about only 300,000 sites. The development of a fully reproducible, scalable, portable workflow allows for easy accessible updates of integrative views of all current experiments. The integrated results for the honeybee are consistent with genetic determination of methylation site accessibility by yet uncharacterized sequence features and physiological control of methylation levels at those sites.
Publisher: Wiley
Date: 02-09-2021
DOI: 10.1111/IMB.12732
Abstract: Social insects depend on communication to regulate social behaviour. This also applies to their larvae, which are commonly exposed to social interactions and can react to social stimulation. However, how social insect larvae sense their environment is not known. Using RNAseq, we characterized expression of sensory‐related genes in larvae of the ant Formica fusca , upon exposure to two social environments: isolation without contact to other in iduals, and stimulation via the presence of other developing in iduals. Expression of key sensory‐related genes was higher following social stimulation, and larvae expressed many of the same sensory‐related genes as adult ants and larvae of other insects, including genes belonging to the major insect chemosensory gene families. Our study provides first insights into the molecular changes associated with social information perception in social insect larvae.
Publisher: Wiley
Date: 17-12-2021
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 s les 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.
Publisher: Wiley
Date: 04-2019
DOI: 10.1111/MEC.15062
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.
Publisher: Wiley
Date: 05-06-2021
DOI: 10.1002/ECE3.7736
Abstract: Vitellogenin (Vg), a storage protein, has been significantly studied for its egg yolk precursor role in oviparous animals. Recent studies found that vitellogenin and its Vg‐like homologs were fundamentally involved in many other biological processes in social insects such as female caste differences and oxidative stress resilience. In this study, we conducted the first large‐scale molecular evolutionary analyses of vitellogenin coding genes ( Vg ) and Vg‐like genes of bumble bees, a primitively eusocial insect belonging to the genus Bombus. We obtained sequences for each of the four genes ( Vg , Vg‐like‐A , Vg‐like‐B , and Vg‐like‐C ) from 27 bumble bee genomes (nine were newly sequenced in this study), and sequences from the two closest clades of Bombus , including five Apis species and five Tetragonula species . Our molecular evolutionary analyses show that in bumble bee, the conventional Vg experienced strong positive selection, while the Vg‐like genes showed overall relaxation of purifying selection. In Apis and Tetragonula however, all four genes were found under purifying selection. Furthermore, the conventional Vg showed signs of strong positive selection in most subgenera in Bombus , apart from the obligate parasitic subgenus Psithyrus which has no caste differentiation. Together, these results indicate that the conventional Vg , a key pleiotropic gene in social insects, is the most rapidly evolving copy, potentially due to its multiple known social functions for both worker and queen castes. This study shows that concerted evolution and purifying selection shaped the evolution of the Vg gene family following their ancient gene duplication and may be the leading forces behind the evolution of new potential protein function enabling functional social pleiotropy.
Location: France
No related grants have been discovered for Claire Morandin.