- We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - While parasitoids that target aphids have evolved convergently several times, their largest radi- ation is found in the braconid subfamily Aphidiinae, which contains at least 400 described species across 50 genera [9, 19]. - In the wild, both species are found infecting a wide range of aphid species although their host ranges dif- fer, with A. - ervi more specialized on aphids in the Macrosiphini tribe and L. - both reproductive modes and genome- wide heterozygosity are maintained in the species as a whole . - We have examined GC con- tent in the context of host environment, nutrient limitation, and gene expression. - b Life history characteristics of the two species. - we suspect that this may be due to duplications in the assembly, and future work should ad- dress these duplications. - fabarum: 76.3%, Supplementary Table 4) and protein level in the predicted genes (A. - A survey of transposable Elements (TEs) identified a similar overall number of putative TE elements in the two assemblies (A. - Despite this similarity, the overall coverage by repeats is larger in the assembly of L.. - To examine genes that may underlie novel functional adaptation, we identified sequences that are unique within the predicted genes in the A. - This nucleotide bias is accompanied by strong codon bias in the predicted genes, meaning that within the possible codons for each amino acid, the two genomes are almost universally skewed towards the codon(s) with the lowest GC content (measured as Relative Synonymous Codon Usage, RSCU, Fig. - To examine gene families that may have undergone ex- pansions in association with functional divergence and specialization, we identified groups of orthologous genes that have increased and decreased in size in the two ge- nomes, relative to one another. - Putative gene-family expansions would be found in the predicted HOGs, because they are calcu- lated to allow for >. - Proportions of all possible codons, as used in the predicted genes in A. - of the codon. - Among the venom proteins shared between both parasit- oids, a gamma glutamyl transpeptidase (GGT1) was the most abundant protein in the venom of both A. - containing mutations in the active site was also found in the venom of L. - Several LRR pro- teins were found in the venom of L. - We observe significant differences in the GC content of genes biased towards adult or larval L. - In contrast, there is no difference in the nitrogen content of the same set of genes (c, d). - Moreover, these putative venom pro- teins were only identified from transcriptomic data of the venom apparatus and we could not find any corre- sponding annotated gene in the genome. - LRR proteins identified in the analysis with OMA are not related to venom production.. - Among those that could be identified was apolipophorin in the venom of L.. - Among parasitoid wasps, apolipophorin has been described in the venom of the ichneumonid Hypo- soter didymator [75] and the encyrtid Diversinervus ele- gans [76], but its function is yet to be deciphered.. - fabarum ho- mologs for any of the three secreted cysteine-rich toxin- like peptides that are highly expressed in the A. - We searched for immune genes in the two genomes based on a list of 373 immunity related genes, collected primarily from the Drosophila literature (Add- itional file 10). - In the genome of both wasps, some of the genes encoding proteins of the Imd and Toll pathways were absent (Supplementary Table 13, Supplementary Figure 25, Additional file 10). - We found 21 and 25 putative Osiris genes in the A. - Similarly, CSP numbers are in the same range within parasitic wasps (11 and 13 copies here, Table 3).. - Table 3 Summary of manual curations of select gene families in the two parasitoid genomes. - fabarum, and whatever broad pattern underlies the reduction in the gene reper- toire of L. - A phylo- genetic analysis of these genes showed a deeply rooted expansion in the IR genes (Supplementary Figure 29).. - This scaffold carrying the duplication (scaffold2824) is only fragmentary, but a transformer duplicate has also been detected in the tran- scriptome of a member of the A. - ervi, transformer appears to have an internal repeat of the CAM-domain, as is seen in the genus Aso- bara [100]. - this duplication is in- teresting because a duplicated copy of CWC22 is the pri- mary signal of sex determination in the house fly Musca domestica [105]. - Importantly, we found relatively high BUSCO scores in the predicted genes, suggesting that our gene prediction was largely successful and was not impacted by the low GC-content. - One contribution to the overall difference in gene numbers could be in the larger number of orphan genes that were identified in A.. - In the Hessian fly (Mayetiola destructor), fly-encoded F- box/LRR proteins bind with plant-encoded proteins to form a complex that blocks the plant’s immune defenses against the parasitic fly [141]. - Alternatively, the expansion of his- tone genes could be related to their rapid development in hosts, as has been suggested for similar histone ex- pansions in the parasitoid Diadromus collaris [32].. - Glutamyl transpeptidases are the most abundant proteins in the venom of both A. - These venom proteins have been suggested to be involved in the castration of the aphid host after parasitism [145]. - which were previously reported in the venom of A. - ervi might explain these differences in the composition of their CHC profiles, especially their apparent inability to synthesize dienes. - fabarum are involved in the gen- eration of unsaturated CHCs in A. - Strikingly, all of the genes in the Imd pathway, including those encoding GNBP- and PGRP, imd, FADD, Dredd and Relish are missing in some aphid ge- nomes (Acyrthosiphon pisum, Aphis gossypii and Diua- phis noxia and imd is absent in the genomes of A. - This altered immunity might lead to either a decrease in the wasps’ responses to pathogenic bacteria, or they may use other defensive components to fight bacterial infections (perhaps some in common with aphids) that are yet to be discovered. - *More complete methods are available in the Supplemen- tary Material (Additional file 14).. - Wasps sacrificed for CHC analysis were sampled from the first generation reared in the lab on Acyrthosiphon pisum strain LL01 [163], which were mass-reared on Vicia faba cv. - In the lab, parasitoids were reared on H. - In the case of Mate-Pair libraries, removal of improperly oriented read-pairs and removal of Nextera adapters was performed using NextClip [166]. - These error-corrected reads were then used for de novo assembly in the program canu v1.0 [171]. - A first set of genes was predicted by similarity to known proteins or contigs from RNAseq in the same species (described below). - results of the first training re-used to train the software in the second round. - Transcriptomic support for the predicted genes was estimated by mapping available transcriptomic data (same as above) to the re- spective genomes using STAR [193] in the “quantMode”.. - Based on identified features, repeats were classified using Wicker’s TE classification as imple- mented in the PASTEclassifier [204]. - The resulting de novo TE library for the genome was then filtered to re- tain only the elements with at least one perfect match in the genome. - Subsequently, all TEs in the full genomes were annotated with REPET’s TE annotation pipeline.. - Whole genome GC content was calculated by totaling the num- bers of A, C, T, and G in the entire assembly. - In the pre- dicted coding sequences, this was also calculated separately for each predicted gene and third position GC composition was calculated separately in the predicted coding sequences. - insects, we downloaded the 118 available CDS in the RefSeq database of NCBI (date: October 2018) and again calculated per-gene GC content.. - To examine the GC content of life-stage biased tran- scripts, we compared GC content in the genes that were significantly differentially expressed between adults and larvae, and in the most highly expressed genes in this data. - the full analysis pipeline is detailed in the Supplemental Materials. - We identified species specific genes, which we are calling orphan genes, by removing all genes that had hits to any other genes in the nt, nr, and swissprot NCBI database (June 2019). - The mass spectrom- etry proteomics data are deposited in the ProteomeX- change Consortium (proteomecentral.proteomexchange.. - melanogaster Osiris orthologs were searched in the annotated proteomes of A. - Genes involved in the oxidative phosphorylation pathway (OXPHOS) were identified in several steps. - melanogaster refer- ence set that did not have a match in the predicted pro- teins were used as queries to search the genome-assembly (BLASTn), in case they were not in the predicted gene models. - In an iterative approach, we annotated the IRs using known IR sequences from Apis melifera, Drosophila mel- anogaster, Microplitis demolitor and Nasonia vitripennis as queries to identify IRs in the genomes of A. - Then, we inspected and edited homologous gene models from each tool in the Apollo genome browser to adjust for proper splice sites,. - 006562865) in the honeybee A. - mellifera [240] and three copies (NP_001164521,XP XP in the wasp N. - 1), has become redundant in the list of DNA methyltrans- ferase genes as it methylates tRNA instead, but was sur- veyed here as a positive control (N. - Fasta file containing the 2568 orphan genes identified in the A. - Fasta file containing the 968 orphan genes identified in the L. - Details of annotated OXPHOS genes, including duplications in the assembly.. - Evolutionary history of the Hymenoptera. - The diversity and fitness effects of infection with facultative endosymbionts in the grain aphid, Sitobion avenae. - Host-instar selection in the aphid parasitoid Monoctonus paulensis (Hymenoptera: Braconidae, Aphidiinae): a preference for small pea aphids. - The genomic features of parasitism, polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum. - A novel RNA virus in the parasitoid wasp Lysiphlebus fabarum: genomic structure, prevalence, and transmission.. - Venom gland extract is not required for successful parasitism in the polydnavirus- associated endoparasitoid Hyposoter didymator (Hym. - Drosophila immune response: from systemic antimicrobial peptide production in fat body cells to local defense in the intestinal tract. - Function of the Drosophila pattern-recognition receptor PGRP-SD in the detection of gram-positive bacteria. - Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. - Seasonal phenotype-specific transcriptional reprogramming during metamorphosis in the European map butterfly Araschnia levana. - Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. - A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena. - Gene set of chemosensory receptors in the polyembryonic endoparasitoid Macrocentrus cingulum. - Sex determination in the Hymenoptera. - Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. - Gene family evolution in the pea aphid based on chromosome-level genome assembly. - Origin of an alternative genetic code in the extremely small and GC – rich genome of a bacterial symbiont.. - Comparative genome analysis reveals an absence of leucine-rich repeat pattern-recognition receptor proteins in the kingdom Fungi. - A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. - A γ -glutamyl transpeptidase of Aphidius ervi venom induces apoptosis in the ovaries of host aphids. - Diversity in symbiont consortia in the pea aphid complex is associated with large phenotypic variation in the insect host. - Locating proteins in the cell using TargetP, SignalP and related tools
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