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Micro-RNA expression profile of chicken small intestines during Eimeria necatrix infection.

ABSTRACT: Eimeria necatrix is a high pathogenic pathogen second to Eimeria tenella causing chicken coccidiosis. However, the precise underlying molecular mechanisms of interaction between E. necatrix and chickens are not fully understood. Accumulating evidences suggest that micro-RNAs (miRNAs) play pivotal regulatory roles in various diseases, including parasitic diseases. In the present study, the expression profile of miRNAs in Hy-line variety white chicken small intestines infected with E. necatrix was studied by using deep sequencing. A total of 35 miRNAs (including 16 significantly upregulated and 19 significantly downregulated miRNAs) were significantly differentially expressed (DE) in infected tissues at 108 h post-infection (pi). Real-time polymerase chain of 10 miRNAs (including 5 upregulated and 5 downregulated) randomly selected successfully confirmed the effectiveness of deep sequencing. Target prediction showed that 4,568 mRNAs could be regulated by 21 (including 12 upregulated and 9 downregulated) of 35 differentially expressed miRNAs. Functional analysis indicated that target genes of these differentially expressed miRNAs would be involved in pathways related to infection of E. necatrix, including cell differentiation, adhesion, proliferation, and apoptosis (e.g., MAPK signaling pathway and PPAR signaling pathway). To our best knowledge, this is the first study on the miRNA expression profile of small intestines during E. necatrix infection, and the findings in the present study suggested that these DE miRNAs would play important regulatory role in the interaction between E. necatrix and chicken intestines.

SUBMITTER: Liu TL

PROVIDER: S-EPMC7597538 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Micro-RNA expression profile of chicken small intestines during Eimeria necatrix infection.

Liu Ting-Li TL Fan Xian-Cheng XC Wang Yi Y Wang Yu-Xin YX Wang Jun-Wei JW Song Jun-Ke JK Zhao Guang-Hui GH

Poultry science 20200311 5

Eimeria necatrix is a high pathogenic pathogen second to Eimeria tenella causing chicken coccidiosis. However, the precise underlying molecular mechanisms of interaction between E. necatrix and chickens are not fully understood. Accumulating evidences suggest that micro-RNAs (miRNAs) play pivotal regulatory roles in various diseases, including parasitic diseases. In the present study, the expression profile of miRNAs in Hy-line variety white chicken small intestines infected with E. necatrix was ...[more]

PMID: 32359579

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Project description:BACKGROUND:Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear. METHODS:The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique. RESULTS:After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 sense-overlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection. CONCLUSIONS:To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.

Project description:Eimeria is a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic losses. Eimeria species have complex life-cycles consisting of three developmental stages. However, the molecular basis of the Eimeria reproductive mode switch remains an enigma.Total RNA extracted from second- (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix was subjected to transcriptome analysis using RNA sequencing (RNA-seq) followed by qRT-PCR validation.A total of 6977 and 6901 unigenes were obtained from MZ-2 and MZ-3, respectively. Approximately 2053 genes were differentially expressed genes (DEGs) between MZ-2 and MZ-3. Compared with MZ-2, 837 genes were upregulated and 1216 genes were downregulated in MZ-3. Approximately 95 genes in MZ-2 and 48 genes in MZ-3 were further identified to have stage-specific expression. Gene ontology category and KEGG analysis suggested that 216 upregulated genes in MZ-2 were annotated by 70 GO assignments, 242 upregulated genes were associated with 188 signal pathways, while 321 upregulated genes in MZ-3 were annotated by 56 GO assignments, 322 upregulated genes were associated with 168 signal pathways. The molecular functions of upregulated genes in MZ-2 were mainly enriched for protein degradation and amino acid metabolism. The molecular functions of upregulated genes in MZ-3 were mainly enriched for transcriptional activity, cell proliferation and cell differentiation.To the best of our knowledge, this is the first RNA-seq data study of the MZ-2 and MZ-3 stages of E. necatrix; it demonstrates a high number of differentially expressed genes between the MZ-2 and MZ-3 of E. necatrix. This study forms a basis for deciphering the molecular mechanisms underlying the shift from the second to third generation schizogony in Eimeria. It also provides valuable resources for future studies on Eimeria, and provides insight into the understanding of reproductive mode plasticity in different Eimeria species.

Dataset Information

Micro-RNA expression profile of chicken small intestines during Eimeria necatrix infection.

Publications

Micro-RNA expression profile of chicken small intestines during Eimeria necatrix infection.

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