Non-coding RNAs identification and regulatory networks in pathogen-host interaction in the microsporidia congenital infection

Abstract

Background The interaction networks between coding and non-coding RNAs (ncRNAs) including long non-coding RNA (lncRNA), covalently closed circular RNA (circRNA) and miRNA are significant to elucidate molecular processes of biological activities and interactions between host and pathogen. Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-feeding industry. However, little is known about ncRNAs that take place in the microsporidia congenital infection. Here we conducted whole-transcriptome RNA-Seq analyses to identify ncRNAs and regulatory networks for both N. bombycis and host including silkworm embryos and larvae during the microsporidia congenital infection. Results A total of 4,171 mRNAs, 403 lncRNA, 62 circRNAs, and 284 miRNAs encoded by N. bombycis were identified, among which some differentially expressed genes formed cross-talk and are involved in N. bombycis proliferation and infection. For instance, a lncRNA/circRNA competing endogenous RNA (ceRNA) network including 18 lncRNAs, one circRNA, and 20 miRNAs was constructed to describe 14 key parasites genes regulation, such as polar tube protein 3 (PTP3), ricin-B-lectin, spore wall protein 4 (SWP4), and heat shock protein 90 (HSP90). Regarding host silkworm upon N. bombycis congenital infection, a total of 14,889 mRNAs, 3,038 lncRNAs, 19,039 circRNAs, and 3,413 miRNAs were predicted based on silkworm genome with many differentially expressed coding and non-coding genes during distinct developmental stages. Different species of RNAs form interacting network to modulate silkworm biological processes, such as growth, metamorphosis and immune responses. Furthermore, a lncRNA/circRNA ceRNA network consisting of 140 lncRNAs, five circRNA, and seven miRNAs are constructed hypothetically to describe eight key host genes regulation, such as Toll-6, Serpin-6, inducible nitric oxide synthase (iNOS) and Caspase-8. Notably, cross-species analyses indicate that parasite and host miRNAs play a vital role in pathogen-host interaction in the microsporidia congenital infection. Conclusion This is the first comprehensive pan-transcriptome study inclusive of both N. bombycis and its host silkworm with a specific focus on the microsporidia congenital infection, and show that ncRNA-mediated regulation plays a vital role in the microsporidia congenital infection, which provides a new insight into understanding the basic biology of microsporidia and pathogen-host interaction.

Transcriptomic changes in the microsporidia proliferation and host responses in congenitally infected embryos and larvae

“…All RNA-seqs are available under the Sequence Read Archive (SRA) with the BioProject accession number (PRJNA953616) as previously described [ 15 ]. The data includes 12 N. bombycis -infected silkworm samples and 12 normal control silkworm samples.…”

“…Samples were collected from individuals at 5 days in the embryos (NI-E5), 1 day in the larvae (NI-L1), 5 days in the larvae (NI-L5), and 10 days in the larvae (NI-L10). RNA extraction, library construction, and sequencing were conducted as previously described [ 15 ].…”

“…RNA-seq analysis of the pathogen and host was conducted by Gene Denovo Biotechnology Co. (Guangzhou, China) as previously described [ 15 ]. Expression values were calculated as fragment per kilobase per million fragments mapped (FPKM) and normalized by totals per million read.…”

“…Several intracellular parasites, including Leishmania , E. falciformis , and Toxoplasma gondii , as well as their respective hosts, have been studied by dual RNA-seq analyses, which have successfully identified important coding and noncoding genes expressed by both the host and pathogen during infection [ 10 – 14 ]. We also used high-throughput RNA sequencing to investigate the non-coding RNAs of both the host and pathogen during N. bombycis congenital infection in silkworm embryos and larvae [ 15 ]. In our current study, we aim to further elucidate pathogen proliferation and host responses during congenital infection in silkworm embryos and larvae using a dual RNA-seq approach.…”

“…In invertebrates, B. mori has been widely used to study disease pathogenicity [ 20 ]. N. bombycis , an important pathogen of silkworms, can infect silkworm embryos and induce immunosuppression in the host, and during the stages of larvae development, N. bombycis proliferates and activates host immune systems [ 15 ]. A similar phenomenon has also been reported in the zebrafish embryos and larvae infected with M. marinum [ 19 ].…”