Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain
- Received Date: 05 January 2020
- Accepted Date: 07 March 2020
- Published Date: 08 April 2020
Abstract: It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August 2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019). ASF is an acute febrile, hemorrhagic and fulminating infectious disease, and would reach 100% case fatality rate to pigs (Gallardo et al. 2015). The causative pathogen, African swine fever virus (ASFV), is a doublestranded DNA virus with a genome of 170–193 kb belonging to the Asfarviridae family (Galindo and Alonso 2017; Gallardo et al. 2015). A recent study has revealed that ASFV maintains a core genome of 102 ORFs and has 168 dispensable genes (Wang et al. 2019). Thus, the complexed genomic features of ASFV require more attentions. By using the next generation sequencing (NGS) and the single molecule real-time sequencing (SMRT-seq), a couple of Chinese ASFV genomes have been uncovered (Bao et al. 2019; Wen et al. 2019; Jia et al. 2019). Compared to NGS, SMRT-seq has the advantage of long read length and can generate sequencing data containing the original single base modification information, which can be identified through the state-of-art bioinformatic procedures (Senol Cali et al. 2019; Simpson et al. 2017). DNA methylation is a chemical modification common in animal and plant genomes. It refers to the catalytic transfer of methyl groups on active methyl compounds (such as s-adenosine methionine) to other compounds under the catalysis of DNA methyltransferase (DNMT), mainly forming 5-methylcytosine (5-mC), 6-methyladenine (6-mA), 5-hydroxymethylcytosine (5-hmC), etc. DNA methylation, which triggers the epigenetic regulatory mechanism, has been proved to play important roles in gene expression and regulation, embryonic development, and disease-related aspects (Gouil and Keniry 2019). Whether ASFV genome has DNA methylation and epigenetic regulation is to be discerned.