Analysis Of Expression Profiles Of Lncrnas,Mirnas And CircRNAs In Chicken Intestines Infected With Eimeria Necatrix

Eimeria necatrix,one of the main pathogenic species causing chicken coccidiosis,usually inhabits in the epithelial cells of the small intestine and cecum of chickens,resulting in severe bleeding of the damaged intestine.The common clinical symptoms in infected chickens were diarrhea,bloody flux and poor growth,with a little high morbidity and mortality,posing a serious threat to the chicken breeding.At present,the prevention and treatment of this disease mainly depends on drugs and vaccines.Although the drugs have good anti-coccidial effect,drug residues and resistance will be introduced.Vaccines can effectively avoid many side effects caused by chemical drugs,but they have disadvantages such as high cost,easy to spread pathogen,and inadequate immune protection.Recent studies have shown that noncoding RNA(ncRNA)played important regulatory roles in interaction of host-parasite.Especially,the long non-coding RNA(lncRNA),Circular RNA(CircRNA)and microRNA(miRNA)are involved in the occurrence and development of many diseases,and have also been identified as potential targets for various diseases and biomarkers for diagnosis and prognosis.In the present study,E.necatrix infecting chickens were used as a model to study the expression profiles of whole transcriptome in chicken small intestines associated with E.necatrix infection by using the RNA-seq technology.1.The expression profiles of mRNA and lncRNA in the small intestine of chickens infected with E.necatrix were obtained.Ten-day chickens were orally infected with 8000 E.necatrix oocysts and were the middle segment of small intestines of these chickens were collected at 108 h post infection(hpi)for RNA-seq analysis.A total of 1543 mRNAs(707 upregulated and 836 down-regulated)and 95 lncRNAs(49 up-regulated and 46 down-regulated)were significantly differentially expressed.The co-expression network analysis showed 37134 co-expression relationships between these lncRNAs and mRNAs.Of them,73 mRNAs were cis-regulated by 38 lncRNAs and 1453 mRNAs were trans-regulated by 87 lncRNAs.Analysis of GO function and KEGG pathway indicated that the target genes of these differentially expressed lncRNAs were significantly enriched in immune pathways related to E.necatrix infection,such as AMPK,PPAR and JAK-STAT.2.The expression profiles of miRNA in the small intestines of chickens infected with E.necatrix were obtained.A total of 1266 miRNAs were identified in the middle segments of small intestine of chickens,including 663 known miRNAs and 603 novel miRNAs.Further studies showed that 35 miRNAs(16 up-regulated and 19 down-regulated)were significantly differentially expressed during E.necatrix infection.Functional analysis revealed that 4568 target mRNAs of 21 miRNAs were significantly enriched in 2047 GO terms(transcription,post-transcriptional regulation and adhesion molecular connection,etc.)and 54 KEGG pathways(calcium signaling pathway,MAPK signaling pathway and insulin signaling pathway,etc.).3.The expression profiles of CircRNAs in the small intestines of chickens infected with E.necatrix were obtained.A total of 4153 CircRNAs sequences were identified in the middle segments of small intestines of chickens,and 13 CircRNAs(nine up-regulated and four downregulated)were differentially expressed during E.necatrix infection.Functional analysis revealed that these CircRNA-derived genes were mainly enriched in the positive regulation of NF-?B signaling pathway and phosphatidylinositol signaling pathway.The network analysis of CircRNA-miRNA-mRNA showed that the differentially expressed CircRNAs in this study may indirectly regulate 62 differentially expressed target mRNAs by sponging two differentially expressed miRNAs,and these target mRNAs were mainly enriched in MAPK,JAK-STAT pathways.In summary,the RNA-seq technology was used to analyze the middle segments of small intestines of chickens infected with E.necatrix,and the expression profiles of mRNAs,lncRNAs,miRNAs and CircRNAs in the small intestines of chickens were changed during E.necatrix infection.Functional analysis showed that these RNAs might be involved in the interaction between E.necatrix and the small intestines of chickens.These results provide basic data for deep revealment of interaction mechanism between E.necatrix and chickens.