Comment[ArrayExpressAccession] E-GEOD-76164 MAGE-TAB Version 1.1 Public Release Date 2015-12-19 Investigation Title Testing the Kinship Theory of Intragenomic Conflict in Honey Bees (Apis mellifera) Comment[Submitted Name] Testing the Kinship Theory of Intragenomic Conflict in Honey Bees (Apis mellifera) Experiment Description Sexual reproduction brings genes from two parents – matrigenes and patrigenes – into one individual. These genes, despite being unrelated, should show nearly perfect cooperation because each gains equally through production of offspring. However, an individual’s matrigenes and patrigenes can have different probabilities of being present in other relatives, so that kin selection could act on them differently. Such intragenomic conflict could be implemented by partial or complete silencing (imprinting) of an allele by one of the parents. Evidence supporting this theory is seen in offspring-mother interactions, with patrigenes favoring acquisition of more of the mother's resources if some of the costs fall on half siblings who do not share the patrigene. The kinship theory of intragenomic conflict is little tested in other contexts, but it predicts that matrigene-patrigene conflict may be rife in social insects. We tested the hypothesis that honey bee worker reproduction is promoted more by patrigenes than matrigenes by comparing across 9 reciprocal crosses of two distinct genetic stocks. As predicted, hybrid workers show reproductive trait characteristics of their paternal stock, indicating enhanced activity of the patrigenes on these traits, greater patrigenic than matrigenic expression, and significantly increased patrigenic biased expression in reproductive workers. These results support both the general prediction that matrigene-patrigene conflict occurs in social insects and the specific prediction that honey bee worker reproduction is driven more by patrigenes. The success of these predictions suggests that intragenomic conflict may occur in many contexts where matrigenes and patrigenes have different relatednesses to affected kin. Testing the kinship theory of intragenomic conflict in honey bees Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Galbraith Galbraith Grozinger Person First Name David David Christina Person Mid Initials Asher A M Person Email dag5031@gmail.com Person Affiliation Penn State University Person Address Penn State University, 19a Chemical Ecology Lab, University Park, Pennsylvania, USA Person Roles submitter Protocol Name P-GSE76164-4 P-GSE76164-1 P-GSE76164-3 P-GSE76164-2 Protocol Description We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10. The transcriptome sequencing reads were aligned to the most recent honey bee genome assembly (Amel_4.5) using Tophat. The data was normalized using a trimmed mean of M-values (TMM) method. The EdgeR package in R statistical program was used to identify significantly differentially expressed genes. The transcriptome sequencing reads were also aligned to pseudo-parent genomes (reference genome with parental SNPs included, one for paternal and one for maternal) allowing 0 mismatches with Tophat to look at parent specific gene expression. This data can be found in PSGE_sterile.txt and PSGE_reproductive.txt Genome_build: Amel4.5 Supplementary_files_format_and_content: PSGE_gene_expression.txt contains the gene expression data for each individual. PSGE_sterile.txt contains read counts for each sterile individual at each parental snp. PSGE_reproductive.txt contains read counts for each reproductive individual at each parental snp. Each individual had their ovaries dissected to determine if they were reproductive or sterile based on the level of ovary activation. Eviscerated abdomens with attached fat bodies and ovaries from individual bees were dissected in ice-cold RNAlater® (Qiagen, Valencia, CA) and excess RNAlater® was removed from the samples. RNA was isolated using TRIzol® Reagent (Invitrogen, Carlsbad, CA). RNA libraries were prepared for sequencing using standard Illumina protocols Individuals from reciprocal crosses of Africanized and European honey bees were raised in queenless colonies for ~18 days, allowing time for the workers to activate the ovaries and become reproductively active. Protocol Type normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name organism part Experimental Factor Type organism part Comment[SecondaryAccession] GSE76164 Comment[GEOReleaseDate] 2015-12-19 Comment[ArrayExpressSubmissionDate] 2015-12-18 Comment[GEOLastUpdateDate] 2015-12-21 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AdditionalFile:Data1] GSE76164_PSGE_gene_expression.txt Comment[AdditionalFile:Data2] GSE76164_PSGE_reproductive.txt Comment[AdditionalFile:Data3] GSE76164_PSGE_sterile.txt Comment[SecondaryAccession] SRP067582 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR3033249-SRR3033273 SDRF File E-GEOD-76164.sdrf.txt