A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in Cotesia vestalis

Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp

In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C. vestalis genome through a horizontal transfer (HT) event from a dipteran and was later transferred horizontally from C. vestalis to a lepidopteran species. Based on the phylogeny of Hel_c35, we suggested that both HTs occurred in East Asia. We have also anticipated that, as more sequenced genomes from new species become available, more HTs involving Hel_c35 would be detected. Although the inclusion of Hel_c35 as a CvBV segment turned out to be a methodological artifact, the fact that Hel_c35 copies are present in the genomes of C. vestalis and other arthropods still remains. Here, we investigated the evolution of Hel_c35 in arthropods using an updated data set to reassess our previous findings. Most species (95%) included in the present work had their genomes sequenced after our initial study was published, thus representing new descriptions of taxa harboring Hel_c35. Our results expand considerably the number of putative HTs involving Hel_c35, with up to dozens of previously undescribed events, and suggest that the most recent HTs associated with C. vestalis took place in Europe. Considering the phylogenetic distribution of Hel_c35, and the evidence that its DNA sequences are present in the calyx fluid of C. vestalis and tissues from its parasitized host, we argue that many HT events were favored by the behavior of this wasp.

Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize

The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.

The genomic survey of Tc1-like elements in the silkworm microsporidia Nosema bombycis

BACKGROUND

Microsporidia Nosema bombycis is the destructive pathogen in the production of sericulture. The Tc1/mariner elements belong to important component of DNA transposon.

METHODS

The genomic data of N. bombycis and related Nosema species were screened to identify the Tc1-like elements and analyzed the phylogenetic relationship, based on bioinformational analysis. High-throughput data of transcriptomes and small RNAs were used to evaluate the expressed level and potential rasiRNAs for the Tc1-like elements of N. bombycis.

RESULTS

Twelve complete Tc1-like elements belonging to DD34,E clade is confirmed in the whole genome of N. bombycis, and divided into two branches. Six of them are sole in N. bombycis and thereby would be the molecular marker to differentiate this species from others Nosema spp. Most of the elements have the transcriptional active and are the source of sRNAs.

CONCLUSION

Abundant Tc1-like elements in N. bombycis reflect the expansion of transposons for this genomic characters, comparing with others Nosema spp. The finding of distribution, phylogeny and potential functional activity for Tc1Nbs in N. bombycis will help understanding the role of the DNA transposon in genomic evolution of microsporidia.

Giant Transposons in Eukaryotes: Is Bigger Better?

Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.

Drosophila parasitoid wasps bears a distinct DNA transposon profile

BACKGROUND

The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species.

RESULTS

The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission.

CONCLUSION

Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution.