Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different...

Area of Science:

• Parasitology
• Genomics
• Molecular Biology

Background:

• Eimeria necatrix is a highly pathogenic parasite causing significant chicken mortality.
• Despite genome sequencing, its mRNA transcript sequences and structures are not fully understood, hindering biomarker and drug target discovery.

Purpose of the Study:

• To comprehensively characterize the transcriptome and transcript structures of Eimeria necatrix second-generation merozoites (MZ-2).
• To identify novel isoforms, alternative splicing (AS) events, alternative polyadenylation (APA) sites, fusion transcripts, transcription factors (TFs), and long non-coding RNAs (lncRNAs).

Main Methods:

• High-quality RNA extraction from E. necatrix MZ-2.
• Combined single-molecule real-time (SMRT) and Illumina sequencing for transcript generation.
• Comparative analysis with previous SMRT sequencing data from sporozoites (SZ).

Main Results:

• Identification of 21,923 consensus isoforms in MZ-2, including 17,151 novel isoforms of known genes and 3,918 isoforms of novel genes.
• Discovery of numerous AS events, APA sites, fusion transcripts, TFs, and lncRNAs in both SZ and MZ-2 stages.
• Validation of fusion transcripts using reverse transcription-PCR and Sanger sequencing, confirming authenticity.

Conclusions:

• The study provides extensive data on E. necatrix transcript isoforms, lncRNAs, AS, APA, and fusion transcripts.
• This information improves understanding of transcriptional regulation and gene models.
• The findings offer insights into parasite development and potential strategies for coccidiosis control.