Hymenoptera is the second largest order of insects after Coleoptera. It is estimated that Hymenoptera consists of one million species. However, available genomic resources of Hymenoptera species are not rich. As of December 2021, NCBI had included 228 complete genomes of Hymenoptera species (including 55 Formicidae species), but none of these genomes is from the species of family Mymaridae. Here we sequenced and assembled the first whole genome of Mymaridae.
80% of the sequenced genomes of Hymenoptera species are between 180 and 340 Mb in size, with a few exceptions [57–59]. The size of A. nilaparvatae genome assembly is 488.8Mb, relatively large in Chalcidoidea. This large genome is likely attributed to the high content of repeat sequences (45.5%), which is higher than the majority of Chalcidoidea insects. Nonetheless, the content of repeat sequences in the genomes of Hymenoptera species can be very low, such as Apidae (< 10%) [60], or very high, such as B. treatae (80.6%). The large genome size of A. nilaparvatae contrasts with its extremely small body size (0.6-0.7mm in body length), suggesting that genome size is not positively correlated with body size. We predicted 16861 genes in the genome of A. nilaparvatae, within the range of 12,000–20,000 genes [60] usually found in Hymenoptera species. Notably, the genomes of Hymenoptera species are generally low in GC content, ranging from 30–45% [61], but A. nilaparvatae even reduces the lower bound to 27.52%. The low GC content in genomes is likely due to GC biased gene transformation and high recombination rate [62].
Previous studies based on transcriptomes have suggested that Chalcidoidea originated at late Jurassic 129-81Mya, and the earliest divergence within Chalcidoidea emerged in early-middle Cretaceous [4, 6]. Our phylogenomic analyses based on whole genomes agree well with previous assessments, that Mymaridae is sister to other groups of Chalcidoidea. We reduced the range of the estimated age of the divergence between Mymaridae and other Chalcidoidea groups from 89 ~ 208 Mya [6] to 116.8-132.1 Mya. The estimates of the mode are well consistent, which is 129 Mya by Peters et al and 126.9 Mya in our study. Our phylogeny also shows difference to the one in Peters et al. (2018). Peters suggested Trichogrammatidae is a basal lineage (second to Mymaridae) in Chalcidoidea [6], but we found Trichogrammatidae is nested deep in Chalcidoidea, sister to Encyrtidae.
The number of chemoreceptor and mechanoreceptor genes differ among species of Hymenoptera, which is related to the complexity of chemoreceptor and mechanoreceptor in these species. Notably, the limitations of available data and method might have hindered accurate identification of these genes. For example, quite a few previous studies were based on low-quality genome assemblies or transcriptomes [21, 25, 28, 29]. We used the latest high-quality genome assemblies to obtain reliable identification of chemoreceptor and mechanoreceptor genes.
OBP is the first soluble chemoreceptor protein found in insects. In Hymenoptera, the number of OBP genes varies greatly among species [25, 63, 64]. We found an expansion of OBP family in Pteromalidae species, relative to other Hymenoptera species. In addition to Pteromalidae, T. pretiosum in Trichogrammatidae also has a large OBP family. The OBP phylogenetic analysis showed long branches in Pteromalidae and T. pretiosum, suggesting of rapid evolution. The number of CSP genes show lower level of differentiation among species. The NPC2 genes are usually found with large number in Chelicerata species, but not in insects [39]. Consistently, we identified less than 10 members of NPC2 family in each of the 13 Hymenoptera species. The numbers of OBP, CSP and NPC2 in A. nilaparvatae are 17, 11 and 4, respectively, within the lower half among the investigated species. Among all species, C. solmsi has the lowest number of the three kinds of soluble protein genes, which may be attributed to its strict specificity to the host ficus [31].
All of the 13 Hymenoptera species have a large OR family but a small GR family, both of which belong to the GPCR superfamily [17]. Tandem duplication has been extensively found in the OR family, and the expansion of OR family is usually accompanied with a deficient of GR family [17]. IR genes belong to the iGluR family. These numbers of IRs in the 13 insect species are less than the numbers of ORs, but more than the numbers of GRs. In addition, the numbers of SNMPs show little difference among Hymenoptera species, and we identified more SNMPs than previous efforts [65, 66].
PPKs play important roles in mechanosensory and other functions. PPKs evolved under the genetic birth-and-death model, which produces lineage-specific expansions that form local clusters in phylogeny. Among all insect orders, Hymenoptera has the fewest PPK proteins [28]. We found only one PPK gene in A. nilaparvatae, the least in the 13 Hymenoptera insects. Similarly, the number of TRP genes in A. nilaparvatae is also the smallest in the 13 species. TRP family is classified into seven subfamilies (TRPC, TRPA, TRPM, TRPML, TRPV, TRPN and TRPP), and TRPC is the “classical TRPs” [67]. The size of the TRP family is generally 13–14 in insect species, and the subfamily TRPP is usually absent in Hymenopteras species [24]. Our phylogenetic of TRPs identified in the 13 species clustered the candidates into five subgroups, with TRPML and TRPV being not distinguishable.
Among all the 13 species, N. vitripennis has the most abundant chemo- and Mechano- sensory genes, consistent with the observation of more gene family expansions than contractions in the CAFÉ analysis. T. pretiosum, another egg parasitoid, has a large number of PPK and TRP genes, as well as abundant chemoreceptor genes. It is likely due to the wide range and complex habitats of the host of T. pretiosum. In contrast, the chemo- and mechano-sensory genes of A. nilaparvatae have degraded, with less copies than other species in Hymenoptera. Interestingly, the range of the host of A. nilaparvatae is very narrow. Similarly, C. solmsi, which is strictly coevolving with the host ficus, also shows a contraction of gene families. This implies a correlation between the numbers of chemoreceptor and mechanoreceptor genes and the single host and simple habitat.