Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

Abstract

Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum. Functional annotation of genes is not fully available for C.floridanum; however, whole genome assembly has been archived. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation, fatty acid biosynthesis, cell morphogenesis in the differentiation and integrin signaling pathways were fluctuated following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis. Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum, and identified transcripts with high similarity to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

Systematic Functional Annotation Workflow for Insects

“…By this procedure, the functional annotation of genes was dramatically improved by using well-annotated species protein sequence datasets compared with the use of only a non-redundant dataset (nr), where so many genes tend to be annotated as “hypothetical proteins” because gene descriptions of related organisms are frequently assigned. The use of silkworms and Japanese stick insects as well as parasitic wasps Copidosoma floridanum made this feature suitable for the functional annotation of insect species [ 38 , 39 ].…”

Systematic functional annotation workflow for insects

“…By this procedure, the functional annotation of genes was dramatically improved by using well-annotated species protein sequence datasets compared with the use of only non-redundant dataset (nr), where so many genes tend to be annotated as ‘hypothetical protein’ because gene descriptions of related organisms are frequently assigned. The use of silkworms and Japanese stick insects as well as parasitic wasps Copidosoma floridanum made this feature suitable for functional annotation of insect species possible [38,39].…”

Long-read genome assembly of the Japanese parasitic waspCopidosoma floridanum(Hymenoptera: Encyrtidae)

“…The process and molecular basis of soldier development in C. floridanum have been described and investigated in the US and Japanese strains 2,8,9 ; however, the development and behavioral patterns of male soldiers differed between the two strains. In the US strain, male soldiers appear in the last larval stage of the host 10 , whereas in the Japanese strain, they appear in the first- or second-instar larvae 11 .…”

“…The process and molecular basis of soldier development of C. floridanum have been described and investigated both in the US and Japanese strain 2,8,9 . The development and behavioral patterns of the male soldiers differ between the two strains.…”

“…The process and molecular basis of soldier development in C. floridanum have been described and investigated mainly in the US and Japanese strains (Ode and Strand 1995;Smith et al 2017;Sakamoto et al 2020). Like other hymenopteran insects (Cook 1993), C. floridanum is haplodiploid species in which the females develop from the fertilized eggs and the males develop from the unfertilized egg (Iwabuchi 2019).…”