Comparison of transcriptome assemblies of Dohne Merino sheep gastrointestinal tissues generated using Illumina and Nanopore MinION Technologies
Transcriptomic studies are essential for understanding metabolic pathways and functional elements of the genome that underpin organisms' phenotypic traits. In this study, the transcriptome of the gastrointestinal tract of Dohne Merino sheep was reconstructed into a comprehensive set of full-length transcripts using RNA-Seq data generated from both Illumina short-read sequencing and Oxford Nanopore Technologies (ONT) MinION long-read sequencing. The objective of the study was to compare the performance of these sequencing technologies in generating transcriptome assemblies. Total RNA was extracted from the gastrointestinal tissues (abomasum, duodenum, ileum and jejunum) of six Dohne Merino sheep for sequencing. The Illumina short-read assembly comprised 447,469,614 nucleotide bases, whereas the ONT long-read assembly contained 3,269,201 bases. The long-read assembly showed higher contiguity with an N50 of 2,801 bp, compared to 2,167 bp for the short-read assembly. Assembly quality and completeness were evaluated against the Ovis aries reference genome (v4.0), revealing an overall alignment rate of 80.31% for Illumina short reads and 98.56% for ONT long reads. To reduce sequencing errors associated with long-read technologies, the ONT assembly was polished using Illumina short reads; however, no substantial improvement in the draft assembly was observed. Overall, the results indicate that while ONT MinION long reads generated longer and more contiguous transcripts, the transcriptome assembly produced using MinION data alone showed limitations for genome-guided annotation in this dataset. These findings highlight the strengths and limitations of Illumina and ONT sequencing technologies for transcriptome assembly in sheep.