Key result
Combined short and long-read sequencing reveals complex transcriptomic architecture in African swine fever virus.
Why the study?
Despite the agricultural importance of African swine fever virus, little is known about the fundamental molecular mechanisms of this pathogen.
Combined short and long-read sequencing reveals a highly complex transcriptomic architecture of African swine fever virus, challenging the current view of monocistronic transcripts.
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for comprehensively annotating transcriptomes. Long-read sequencing (LRS) can overcome some of SRS's limitations, but it also has drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the ASFV transcriptomic atlas. This work identified many novel transcripts and transcript isoforms and annotated the precise termini of previously described RNAs. This study identified a novel species of ASFV transcripts, the replication origin-associated RNAs. Additionally, we discovered several nested genes embedded into larger canonical genes. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps was also discovered.
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Torma et al. (2021) studied African swine fever virus. Combined short-read and long-read sequencing was evaluated on Transcriptomic atlas construction. Combined short and long-read sequencing of the African swine fever virus revealed a complex transcriptomic architecture, including novel transcripts, polycistronism, and transcriptional overlaps.
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