Abstract
BackgroundCryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were still not available. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in regulating occurrence and progression of many diseases and are identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of host mRNAs, lncRNAs and circRNAs associated with C. baileyi infection were investigated for the first time.ResultsThe tracheal tissues of experimental (C. baileyi infection) and control chickens were collected for deep RNA sequencing, and 545,479,934 clean reads were obtained. Of them, 1376 novel lncRNAs were identified, including 1161 long intergenic non-coding RNAs (lincRNAs) and 215 anti-sense lncRNAs. A total of 124 lncRNAs were found to be significantly differentially expressed between the experimental and control groups. Additionally, 14,698 mRNAs and 9085 circRNAs were identified, and significantly different expressions were observed for 1317 mRNAs and 104 circRNAs between two groups. Bioinformatic analyses of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for their targets and source genes suggested that these dysregulated genes may be involved in the interaction between the host and C. baileyi.ConclusionsThe present study revealed the expression profiles of mRNAs, lncRNAs and circRNAs during C. baileyi infection for the first time, and sheds lights on the roles of lncRNAs and circRNAs underlying the pathogenesis of Cryptosporidium infection.
Highlights
Cryptosporidium baileyi is the most common Cryptosporidium species in birds
Considering the characteristics of Long non-coding RNAs (lncRNAs) sequences (≥ 200 nt, exon count ≥2) and their differences from other classes of RNAs, the transcripts were classified into different subtypes using both Scripture beta2 and Cufflinks (v2.1.1). 93.98% of the identified transcripts (50,857) were known as the reference transcripts, whereas 6.02% (3061) were the presumed lncRNAs
To further confirm these 3061 lncRNAs, 2823 transcripts were obtained after filter of the low expression transcripts with Fragments per kilobase for a million reads (FPKMs) < 0.5
Summary
Cryptosporidium baileyi is the most common Cryptosporidium species in birds. effective prevention measures and treatment for C. baileyi infection were still not available. Previous studies have indicated that non-coding RNA (ncRNA) molecules were involved in host-Cryptosporidium interaction process, and aberrant expressions of microRNAs (miRNAs) were detected in C. parvum infecting epithelial cells [25, 26]. Previous studies have showed that it could harbor specific miRNAs as miRNA sponges [43,44,45] to suppresses miRNA activity, resulting in increased levels of miRNA targets, influence the expression of cytokines [46], promote cell cycles and inhibit cell apoptosis to act as a candidate oncogene [47, 48] Both lncRNAs and circRNAs have been identified as effective biomarkers for diagnosis and prognosis of diseases [49, 50]. Our findings would provide baseline data for developing novel diagnostic and therapeutic targets for avian cryptosporidiosis
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