Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms

Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.

The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

Characterisation of the fig-fig wasp holobiont

Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.

Differences in susceptibility to chlorantraniliprole between Chilo suppressalis (Lepidoptera: Crambidae) and two dominant parasitic wasps collected from Sichuan Province, China

Chilo suppressalis Walker (Lepidoptera: Crambidae) is one of the most destructive pests occurring in the rice-growing regions of Asia. Parasitoids, mainly egg parasitoids, have been of interest for several years even with practical used cases. Therefore, the potential impact of insecticides on natural enemies needs great attention. In this study, chlorantraniliprole was evaluated for its impact on C. suppressalis and two dominant parasitic wasps. Bioassays showed that chlorantraniliprole had negligible toxicity to Eriborus terebrans but was significantly toxic to Chelonus munakatae; the mortality exceeded 50% when the concentration reached 46.83 ng/cm². Enzyme assays suggested that the significantly different carboxylesterase activity may be involved in the high-level detoxification metabolism of E. terebrans. According to the results of enzyme gene correlation analysis, P450s may be the dominant factor in the detoxification metabolism of C. munakatae. In addition, the ryanodine receptor C-terminus of C. suppressalis (CsRyR), C. munakatae (CmRyR) and E. terebrans (EtRyR) were successfully cloned. Different amino acids at resistance mutation I4758 M between susceptible C. suppressalis (I) and parasitic wasps (M) may be related to susceptibility differences. Simulated docking showed that CsRyR and CmRyR can interact with chlorantraniliprole but not EtRyR. More interaction forces were formed between CsRyR and chlorantraniliprole than CmRyR. Furthermore, a Pi-Pi T-shape formed between 73PHE in CsRyR and the benzene ring in chlorantraniliprole. These results indicated that both detoxification metabolism and the target site could mediate the susceptibility difference between C. suppressalis and its parasitic wasps.

Genome-Wide Identification and Analysis of Lipases in Fig Wasps (Chalcidoidea, Hymenoptera)

Simple Summary

Lipases are a large family of enzymes involved in lipid metabolism. Lipids play diverse roles in insect growth and responses to environmental stimuli. Fig wasps are a polyphyletic assemblage of Chalcidoidea that develop in the inflorescences of fig trees. Based on whether they can pollinate, they are separated into pollinator fig wasp (PFW) and non-pollinating fig wasp (NPFW). In this study, we conducted a genome-wide screening of lipases in the 12 fig wasp genomes using bioinformatics tools, including seven PFWs and five NPFWs. In total, 481 lipase genes were identified with the neutral and acid lipases as the most numerous families. NPFWs had significantly more lipases than PFWs. Tandem duplication accounted for the expansion of the gene family. Phylogenetic analysis indicated that the lipase genes were conserved. This study provided evidence of insect metabolism to understand the obligate mutualism between figs and fig wasps. Our results will facilitate the understanding of the molecular mechanism of how lipase proteins contribute to the distinctions of life histories between PFWs and NPFWs.

Abstract

Lipases are the main enzymes involved in lipid metabolism. However, the characteristics of lipases in insects were scarcely investigated. Here, we screened the recently sequenced genomes of 12 fig wasp species consisting of seven pollinator fig wasps (PFWs) and five non-pollinating fig wasps (NPFWs) for the six major lipase gene families. In total, 481 lipase genes were identified, and the two most numerous families were the neutral and acid lipases. Tandem duplication accounted for the expansion of the gene family. NPFWs had significantly more lipases than PFWs. A significant gene family contraction occurred in the clade of PFWs. The difference of lipases between NPFWs and PFWs might contribute to their distinction in life histories and feeding regimes. Phylogenetic analysis showed that the lipase genes of each fig wasp species was almost equally distributed in each clade, indicating that the lipase genes were conserved. The gene structures were similar within each clade, while they were different among clades. Most of the neutral and acid lipases were signal peptides and located extracellularly. The pathways of lipases involved were predicted. This genome-wide study provides a systematic analysis of lipase gene families in 12 hymenopteran insects and further insights towards understanding the potential functions of lipases.

Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans

Telomeres consist of highly conserved simple tandem telomeric repeat motif (TRM): (TTAGG)n in arthropods, (TTAGGG)n in vertebrates, and (TTTAGGG)n in most plants. TRM can be detected from chromosome-level assembly, which typically requires long-read sequencing data. To take advantage of short-read data, we developed an ultra-fast Telomeric Repeats Identification Pipeline and evaluated its performance on 91 species. With proven accuracy, we applied Telomeric Repeats Identification Pipeline in 129 insect species, using 7 Tbp of short-read sequences. We confirmed (TTAGG)n as the TRM in 19 orders, suggesting it is the ancestral form in insects. Systematic profiling in Hymenopterans revealed a diverse range of TRMs, including the canonical 5-bp TTAGG (bees, ants, and basal sawflies), three independent losses of tandem repeat form TRM (Ichneumonoids, hunting wasps, and gall-forming wasps), and most interestingly, a common 8-bp (TTATTGGG)n in Chalcid wasps with two 9-bp variants in the miniature wasp (TTACTTGGG) and fig wasps (TTATTGGGG). Our results identified extraordinary evolutionary fluidity of Hymenopteran TRMs, and rapid evolution of TRM and repeat abundance at all evolutionary scales, providing novel insights into telomere evolution.

Genome-Wide Analysis of Gene Families of Pattern Recognition Receptors in Fig Wasps (Hymenoptera, Chalcidoidea)

Pattern recognition receptors (PRRs) play important roles in detecting pathogens and initiating the innate immune response. Different evolutionary histories of pollinators and non-pollinators may result in different immune recognition systems. A previous study had reported that there were significant differences in peptidoglycan recognition proteins (PGRPs) between pollinators and non-pollinators in gene number and lineage of specific genes. In this study, based on the genomic data of 12 fig wasp species, with seven pollinators and five non-pollinators, we investigated the evolution patterns of PRRs, such as Gram-negative bacteria-binding proteins (GNBPs), C-type lectins (CTLs), scavenger receptors class B (SCRBs), fibrinogen-related proteins (FREPs), galectins, and thioester-containing proteins (TEPs). Our results showed that pollinators had no GNBP, but non-pollinators all had two gene members, which were clustered into two different clades in the phylogenetic tree, with each clade having specific domain and motif characteristics. The analysis of CTL and SCRB gene families also showed that there were lineage-specific genes and specific expansion in non-pollinators. Our results showed that there were significant differences in immune recognition between pollinators and non-pollinators, and we concluded that they had undergone flexible adaptive evolution in different environments. Our study can provide more molecular evidence for future functional studies on the immune system of fig wasps.