Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp

Abstract Social insect reproductives and non‐reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes in obligately social taxa such as honey bees, while relatively few studies have addressed the molecular correlates of reproductive differentiation in species in which the division of reproductive labour is established only in plastic dominance hierarchies. To address this knowledge gap, we generate the first genome for any stenogastrine wasp and analyse brain transcriptomic data for non‐reproductives and reproductives of the facultatively social species Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive ‘queues’ exhibited by social colonies of this species, we show that reproductive division of labour in this species is associated with transcriptomic signatures that are more subtle and variable than those observed in social taxa in which colony living has become obligate; that variation in gene expression among non‐reproductives reflects their investment into foraging effort more than their social rank; and that genes associated with reproductive division of labour overlap to some extent with those underlying division of labour in the separate polistine origin of wasp sociality but only explain a small portion of overall variation in this trait. These results indicate that broad patterns of within‐colony transcriptomic differentiation in this species are similar to those in Polistinae but offer little support for the existence of a strongly conserved ‘toolkit’ for sociality.


Results
A total of 13,137 (76.34%) out of 17,208 proteins had some type of annotation feature derived from one of the annotation resources used in this work.GO terms were assigned to 9,954(57.85%)proteins (Table SC1).Additionally, we were capable of assigning a description (name) to 8,167 proteins using Blast best hit or KEGG.

genes proteins
Total  SC1.Gene and protein annotation statistics.

Domain and family signatures
In this functional annotation we used InterProScan and Batch CD-search software to assign domains and other functional elements to the proteins of interests.InterProScan v.5.19-58 was used to inspect proteins for signatures using all available InterPro databases and scanning applications, in total, 12,665 (73.59 %) proteins have some type of protein signatures.More specifically, 11,152 proteins (68.06%) are annotated with at least one signature coming from one of the most important InterPro databases for functional annotation (i.e.PANTHER, Pfam, TIGRFAM, HAMAP, SUPERFAMILY).

GO terms
We have three different sources of evidence to associate GO terms to our proteins: InterPro, KEGG and p2gpipe (Table SC3), each of this evidence is complementary to each other.In total we managed to associate at least one GO term to 9954 proteins; with 1-24 GO terms per protein.SC3. Source of evidence used for GO terms association and number of transcripts assigned by each of them

Molecular function 8668
Biological process 5915 Cellular component 4308 Table SC4.Number of proteins, associated with each different GO term type.

Proteins with identified transposon activity
We annotated proteins as putative transposons by using annotation signatures that were previously associated to the TEs activity.Within these signatures are the PFAM domainswe're searching for ~80 transposase domains; GO terms GO:0006278(RNA-dependent DNA replication), GO:0015074(DNA integration), GO:0006355(regulation of transcription, DNAtemplated), GO:0004803(transposase activity); and finally we do search for 'retrotransposon/transposase' within definition obtained from the Blast2GO or KEGG.
In total we annotate 489 proteins ( 363 genes) as putative transposons:

PFAM domains 37 GO terms 453
Blast/KEGG definition 3 By three methods 0 By two methods 4 Table SC5.Number of proteins associated with transposon activity.

Associated files
The files containing all the annotation features produced in this work can be downloaded from https://public_docs.crg.es/rguigo/Data/avlasova/FunctionalAnnotation/waspProject/L.flavolineata

Table SC2 .
Table B2 displays the number of proteins containing a signature belonging to each specific InterPro member database.Automatic Batch CD-server was used to scan a set of pre-calculated position-specific scoring matrices with proteins.In total, 11,655 proteins have domain hits and 4,356 proteins have features data.Example of annotated features: active sites, inter-domain contacts, cleavage sites or proline interaction residues.Number of protein signatures identified by InterProScan for each of the InterPro member databases

Table SC4
displays the number of GO terms of each specific type obtained in this work.