Brain microRNAs among social and solitary bees

Abstract

37Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific 38 changes in gene expression, but the key nodes that drive these regulatory changes are largely 39 unknown. We tested the hypothesis that changes in gene regulation associated with social 40 evolution are facilitated by lineage-specific function of microRNAs (miRNAs). Genome scans 41 across 12 bee species showed that miRNA copy-number is mostly conserved and not associated 42 with sociality. However, deep sequencing of small RNAs in six bee species revealed a 43 substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the 44 brain, 24-72% of which did not have homologs in other species. Lineage-specific miRNAs 45 disproportionately target lineage-specific genes, and have lower expression levels than shared 46 miRNAs. The predicted targets of lineage-specific miRNAs are enriched for genes related to 47 social behavior in social species, but they are not enriched for genes under positive selection. 48Together, these results suggest that novel miRNAs may contribute to lineage-specific patterns of 49 social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by 50 selection due to deleterious effects on mRNA targets, and suggest genome structure is not as 51 influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs. 52 53 specific 55 56 57Eusociality has evolved several times in the hymenopteran insects. In its most basic form, 58 this lifestyle involves reproductive queens living with their worker daughters who forego direct 59 reproduction to cooperatively defend the nest, care for their siblings, and forage for the colony. 60 Due to the complex nature of this lifestyle, the evolution of eusociality likely requires 61 modification of molecular pathways related to development, behavior, neurobiology, physiology, 62 and morphology [1]. The evolution of eusociality is thus expected to involve both genetic 63 changes as well as changes in the way the genome responds to the environment [2]. It is 64therefore unsurprising that recent studies aimed at identifying the genomic signatures of eusocial 65 evolution in insects have found that social species share an increased capacity for gene regulation 66 [3,4]. Evidence for this comes from signatures of rapid evolution of genes involved in 67 transcription and translation, gene family expansions of transcription factors, and increasing 68 potential for DNA methylation and transcription factor binding activity in conserved genes. 69Interestingly, while these types of regulatory changes are common to independent origins and 70 elaborations of eusociality, the specific genes and regulatory elements involved are unique to 71 each lineage [3][4][5]. This suggests that lineage-specific processes are influential in generating new 72 patterns of gene regulation that contribute to social behavior. 73 74 Small, non-coding RNAs such as microRNAs (miRNAs) may be an important source of 75 regulatory novel...

Kr-h1 maintains distinct caste-specific neurotranscriptomes in response to socially regulated hormones

“…We analyzed previously published RNA-seq data from ant species with fixed queen-worker (Solenopsis invicta and Monomorium pharaonis) or queenless social systems (Dinoponera quadriceps and Ooceraea biroi). We also analyzed two species of wasps (Polistes dominula and Polistes canadensis) and bees (Bombus terrestris and Megalopta genalis) (Chandra et al, 2018;Kapheim et al, 2020;Marshall et al, 2020;Patalano et al, 2015;Standage et al, 2016;Wang et al, 2020). In all cases, genes differentially expressed between non-reproductive and reproductive individuals overlapped significantly with genes regulated by JH3 and 20E in Harpegnathos neuronal cultures (Figure S3, Venn diagrams).…”

“…Analyses in other Hymenoptera species (Figure S3) For comparisons with other species' RNA-seq data, we used the following RNA-seq SRA datasets and comparisons: B. terrestris (SRP078797), dominant reproductive versus foragers (Marshall et al, 2020); D. quadriceps (SRP044613), alpha versus low (Patalano et al, 2015); M. genalis (SRP079663), queen versus worker (Kapheim et al, 2020); M. pharaonis (SRP239431), queen versus worker (Wang et al, 2020); O. biroi (SRP148603), reproductive versus non-reproductive workers (Chandra et al, 2018); P. canadensis (SRP044613), gyne versus worker (Patalano et al, 2015); P. dominula (SRP061693), gyne versus worker (Standage et al, 2016); S. invicta (SRP148603), queen versus forager (Chandra et al, 2018). Reads were mapped to the current Refseq release of the relevant genome and annotation, and gene-level counts quantified as described for Harpegnathos.…”

Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees (Megachile rotundata)

“…Many (34) of the 72 unique mature miRNA sequences identified in our oocyte and egg samples were previously found in miRNA expression data of M. rotundata brains (Fig. S3) (Kapheim et al 2020). While only 72 unique mature miRNA sequences were identified, we characterized 75 distinct miRNAs for differential expression analysis.…”

“…Reads shorter than 18 bases were discarded, non-nucleotide letters were removed (anything other than the following characters: ATCGUNatcgun), and reads were then collapsed. Next, we identified known miRNAs and discovered novel miRNAs using known precursor sequences from M. rotundata , and the known mature sequences from M. rotundata, Bombus impatiens, B. terrestris, Apis mellifera, Megalopta genalis and Nomia melanderi (Kapheim et al 2020) as inputs alongside our sample sequences to the miRDeep2.pl script of miRDeep2 (Friedländer et al 2011). Next, we ran the quantifier.pl script of miRDeep2 on found known and novel miRNAs for each M. rotundata individual sample to obtain read quantities for each pair of precursor and mature miRNA.…”

“…For the second run, we first compiled a list of the unique novel precursor miRNA sequences from across all samples which passed the aforementioned filtering criteria for the output from the first quantifier.pl run. This list of novel precursor miRNAs was added to the list of known precursor miRNAs of M. rotundata from Kapheim et al (2020), and the composite was used as the species-specific precursor miRNA input for the second run of miRDeep2.pl , without changing any other inputs. We then applied the same filters to compile our final list of miRNAs.…”