A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum

Abstract

Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect–the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.

Conservative route to genome compaction in a miniature annelid

“…By contrast, the evolutionary drivers of genome compaction are more debated and hypotheses are often based on correlative associations 1 ; for example, with changes in metabolic 19 and developmental rates 20 , cell and body sizes 1 , 21 (as in some arthropods 22 , 23 , flatworms 22 and molluscs 24 ) and the evolution of radically new lifestyles, such as powered flight in birds and bats 13 , 25 and parasitism in some nematodes 26 , 27 and orthonectids 28 . However, these correlations often suffer from multiple exceptions; for example, not all parasites have small genomes 27 neither does the insect with arguably the smallest body size have a compact genome 29 and thus they probably reflect lineage-specific specializations instead of general trends in animal evolution. In addition, genomic compaction leading to minimal genome sizes, as in some free-living species of nematodes 30 , tardigrades 31 , 32 and appendicularians 5 , 33 , apparently co-occurs with prominent changes in gene repertoire 34 , 35 , genome architecture (for example, loss of macrosynteny 36 ) and genome regulation (for example, trans -splicing and operons 37 – 39 ), yet these divergent features are also present in closely related species with larger genomes 5 , 32 , 40 .…”

An integrated transcriptomic and proteomic approach to identify the main Torymus sinensis venom components

“…• venom protein D (one protein) identified by the transcriptomic approach, also found in the venom of P. puparum 27 and A. calandrae 31 ; • venom protein F (one protein) identified by the transcriptomic approach, also found in the venom of the wasps M. spermotrophus 129 , Megaphragma amalphitanum, Ceratosolen solmsi, the endoparasitoid Trichogramma pretiosum 203 , and A. calandrae, in this case with a putative role in actin polymerization and in transcription regulation of cholesterol and fatty acid homeostasis 31 ; • venom protein L (one protein) identified by the transcriptomic approach, also found in the venom of P.…”

“…puparum 27 and A. calandrae, in this case with a putative role of OBP 31 ; • venom protein Q (one protein) identified by the transcriptomic approach, also found in the venom of Nasonia giraulti 114 and A. calandrae, in which a seryl-tRNA synthetase domain was detected 31 ; • venom protein R (one protein) identified by the proteomic approach, also found in the venom of P. puparum 27 , N. giraulti 114 , M. amalphitanum, C. solmsi, T. pretiosum 203 , Tetrastichus brontispae 204,205 and M. spermotrophus 129 . RNA sequencing performed on abdomen tissue in Ischnura elegans also revealed a venom protein r-like, a toxin and hemolymph juvenile hormone binding protein, that regulates embryogenesis, larva development and reproductive maturation 206 .…”

Revision of the World Species of Megaphragma Timberlake (Hymenoptera: Trichogrammatidae)

“…Due to their extremely small body size, Megaphragma species have become model organisms for studying the miniaturization of insects [ 15 , 16 ] and solving neurobiological problems [ 17 ]. The general anatomy and anatomical features associated with miniaturization have been described [ 18 ]; the structure of the eye [ 19 ], antenna [ 20 , 21 ], and leg structures used for grooming [ 22 ], and peculiar features of the genome [ 23 , 24 , 25 ] have been studied. Anucleate neurons have been found in three species of Megaphragma [ 18 , 26 ] and the unique phenomenon of lysis of the bodies and nuclei of cells at the pupal stage of development has been described [ 4 ].…”

“…Most Megaphragma species descriptions are very brief, and genetic markers are available only for one named species [ 23 , 25 , 31 ] and three unnamed species [ 32 , 33 ]. Identification keys to species are available only for a few regions and include only selected species.…”