Formica exsecta
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR118156.fastq.gz | Fastqsanger.gz | |||
| DRR118157.fastq.gz | Fastqsanger.gz | |||
| DRR118158.fastq.gz | Fastqsanger.gz | |||
| DRR118159.fastq.gz | Fastqsanger.gz | |||
| DRR118160_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA methylation is an important chromatin modification that is necessary for the structural integrity and proper regulation of the genome for many species. Despite its conservation across the tree of life, little is known about its contribution to complex traits. Reports that differences in DNA methylation between castes in closely related Hymenopteran insects (ants, bees and wasps) contributes to social behaviors has generated hypotheses on the role of DNA methylation in governing social behavior. However, social behavior has evolved multiple times across insecta, and a common role of DNA methylation in social behavior remains outstanding. Using phylogenetic comparative methods we sought to better understand patterns of DNA methylation and social behavior across insects. DNA methylation can be found in social and solitary insects from all orders, except Diptera (flies), which suggests a shared loss of DNA methylation within this order. The lack of DNA methylation is reflected in the absence of the maintenance and de novo DNA methyltransferases (DNMT) 1 and 3, respectively. Interestingly, DNA methylation is found in species without DNMT3. DNA methylation and social behavior (social/solitary) or with division of labor (caste+/caste–) for 123 insect species analyzed from 11 orders are not evolutionary dependent, which is further supported by sequencing of DNA methylomes from 40 species.
2017-02-02 | GSE83497 | GEO
Project description:Formica exsecta Transcriptome or Gene expression
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Project description:Formica exsecta Transcriptome or Gene expression
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Project description:Exogenous material associated with F. exsecta
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Project description:In social insects, workers perform distinct tasks according to the caste they belong to, and workers from different castes differ in their age (nest workers are usually younger than foragers are). The caste shift thus seems inseparable from age, preventing from deciphering the role of labour division and age in regulating individual physiology and ageing rates. We set up an experimental protocol separating age and caste effects by defining four groups of black garden ant (Lasius niger) workers: young foragers (Y.F), old foragers (O.F), young nest workers (Y.NW) and old nest workers (O.NW). Proteomics highlighted differences between individuals according to their age, whereas metabolomics revealed caste-related differences. Our study highlighted that age and caste influence specifically different aspects of the physiology of ant workers.
2023-03-11 | PXD026565 | Pride
Project description:Epigenetic modifications are known to profoundly affect the development and behavior of social insects. In the well-known caste differentiation process of honeybee (Apis mellifera), female larvae with identical genomes are fed royal jellydifferently and develop into either normal workers or into very large, long-lived, and extremely fecund queens, and the queen-worker asymmetry of honeybee is known to be result largely to differential genomic imprinting during larval development that involves DNA methylation-based regulation. The discovery of reversible N6-methyladenosine (m6A) RNA methylation modification has defined a new era for RNA-metabolism-related genetic regulation, yet much remains unknown about m6A-mediated post-transcriptional regulatory mechanisms. Here, we report the first honeybee RNA m6A methylome. Specifically, we used the m6A-seq technique to examine the RNA m6A methylomes of honeybee larvae, including queen and worker larvae at multiple instar stages. We identified multiple conserved features of m6A methylation machinery and transcriptome-wide m6A distribution trends among insect species, and observed that m6A marks exert functions in regulating caste differentiation, with apparently particularly strong functional impacts on fifth instar worker larvae. Functional annotation of differentially methylated candidate caste-differentiation-related transcripts revealed many known regulators of caste differentiation (e.g. ILP-2, p110, PI3K, and JHAMT etc.) as well as the widely-studied Vitellogenin gene, which has not previously been implicated in caste differentiation. As ever-more regulatory roles for m6A marks are discovered, honeybees may become an excellent model studying the biology of such epi-transcriptomic regulatory systems, from embryonic development through holometabolous caste-specific development and on towards behavior and the emergent social hierarchies underlying eusociality in animals.
2020-12-13 | GSE137000 | GEO
Project description:Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
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Project description:Phenotypic variation arises from interactions between genotype and environment, although how variation is produced and then maintained remains unclear. The discovery of the nest-mate recognition system in Formica exsecta ants has allowed phenotypic variation in chemical profiles to be quantified across a natural population of 83 colonies. We investigated if this variation was correlated or not with intrinsic (genetic relatedness), extrinsic (location, light, temperature), or social (queen number) factors. (Z)-9-Alkenes and n-alkanes showed different patterns of variance: island (location) explained only 0.2 % of the variation in (Z)-9-alkenes, but 21-29 % in n-alkanes, whereas colony of origin explained 96 % and 45-49 % of the variation in (Z)-9-alkenes and n-alkanes, respectively. By contrast, within-colony variance of (Z)-9-alkenes was 4 %, and 23-34 % in n-alkanes, supporting the function of the former as recognition cues. (Z)-9-Alkene and n-alkane profiles were correlated with the genetic distance between colonies. Only n-alkane profiles diverged with increasing spatial distance. Sampling year explained a small (5 %), but significant, amount of the variation in the (Z)-9-alkenes, but there was no consistent directional trend. Polygynous colonies and populous monogynous colonies were dominated by a rich C23:1 profile. We found no associations between worker size, mound exposure, or humidity, although effect sizes for the latter two factors were considerable. The results support the conjecture that genetic factors are the most likely source of between-colony variation in cuticular hydrocarbons.
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