Short and Long-Read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and the Host Cells

Olasz, Ferenc and Tombácz, Dóra and Torma, Gábor and Csabai, Zsolt and Moldován, Norbert and Dörmő, Ákos and Prazsák, István and Mészáros, István and Magyar, Tibor and Tamás, Vivien and Zádori, Zoltán and Boldogkői, Zsolt (2020) Short and Long-Read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and the Host Cells. Frontiens in Genetics, 11.

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Abstract

To provide a detailed transcription map about the transcription dynamics of the African Swine Fever Virus, we performed multiplatform sequencing using both next-generation short-read sequencing (SRS) and third-generation long-read sequencing (LRS) techniques. The presented dataset represent a key resource for studying the ASFV transcriptome at different time points after infection, and of the effect of infection on the host gene expression. Regarding the SRS approach, the MiSeq instrument (Illumina) was used , whereas we applied the MinION portable sequencer from Oxford Nanopore Technologies (ONT) for full-length sequencing. The random-primed SRS library was run on a single MiSeq v3 flow cell, whereas three different ONT libraries [direct RNA sequencing (dRNA-Seq), direct cDNA sequencing (dcDNA-Seq) and amplified cDNA sequencing) were sequenced on three individual flow cells. Altogether the three LRS experiments resulted in 20,021,413 sequencing reads, of which 139,711 aligned to the viral genome (MN715134.1). The longest average read length was obtained using the dcDNA technique (1,299 bp). The average length for the amplified approach ranged between 598 and 1,017 bp, whereas the dRNA-Seq resulted in an average read length of 953 bp.

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