Abstract
BackgroundEimeria 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.MethodsThe 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.ResultsAfter 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.ConclusionsTo 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.
Highlights
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 underly‐ ing molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed
Eimeria necatrix infection model Eimeria necatrix used in the present study was isolated from the small intestines of sick chickens presented to the clinic (Baoji, Shaanxi, China), purified and propagated by using the single-oocyst method described previously [40, 41], and identified by using the speciesspecific PCR and sequencing.The purified oocysts were passaged in 10-day-old Hy-line variety white specific-pathogen-free (SPF) chickens under a specific pathogen- and coccidia-free environment, and fresh fecal samples were collected for purifying oocysts using the salt-floatation technique
Transcriptomic sequencing data analysis In the present study, the Illumina sequencing generated 594.8 M raw reads from six chicken intestinal samples, and the number of original sequences for each sample ranged from 98.42 M to 99.77 M
Summary
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 underly‐ ing molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Chicken coccidiosis, caused by Eimeria spp., is one of the most common diseases in broilers and laying hens, seriously affecting weight gains and leading to death of birds [1, 2]. The economic losses caused by chicken coccidiosis were estimated to over 3 billion USD per year worldwide and approximately 30–60 million USD have been spent to control this disease annually in China [5,6,7]. The prophylactic use of anticoccidial drugs or vaccines of precocious, attenuated parasites, and wild type vaccine formulations are common strategies to control chicken coccidiosis in clinic [8,9,10,11]. Development of novel strategies for controlling coccidiosis is urgently needed
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