Article ; Online: Impacts of reference selection on the assembly of suspicious coronavirus genome.
Journal of bioinformatics and computational biology
2021 Volume 19, Issue 3, Page(s) 2140005
Abstract: ... of suspicious coronavirus (CoV) found in pangolins, SARS-CoV-2 was used as a reference in most of the previous ... genome assembly. We explored various representative CoVs as the reference genome, and found significant ... considered as a reference for assembling suspicious CoV found in pangolins and other potential ...
| Abstract | The pandemic caused by SARS-CoV-2 has had a significant impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins are considered as a potential intermediate host. To assemble the genome of suspicious coronavirus (CoV) found in pangolins, SARS-CoV-2 was used as a reference in most of the previous studies, implicitly assuming the pangolin CoV and SARS-CoV-2 are the closest neighbors in evolution. However, this assumption may not be true. We investigated how the choice of reference genome affected the resulting CoV genome assembly. We explored various representative CoVs as the reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as a reference showed better statistics in total length, N50, and pairwise distance reconstruction (PDR) scores than the assembly guided by SARS-CoV-2, indicating that RaTG13 may be a better reference. Therefore, RaTG13 should also be considered as a reference for assembling suspicious CoV found in pangolins and other potential intermediate hosts. |
|---|---|
| MeSH term(s) | Animals ; Coronavirus/genetics ; Coronavirus/isolation & purification ; Genome, Viral ; Genomics/methods ; Genomics/standards ; Pangolins/virology ; Phylogeny ; SARS-CoV-2/genetics |
| Language | English |
| Publishing date | 2021-05-06 |
| Publishing country | Singapore |
| Document type | Journal Article |
| ZDB-ID | 2115015-1 |
| ISSN | 1757-6334 ; 0219-7200 |
| ISSN (online) | 1757-6334 |
| ISSN | 0219-7200 |
| DOI | 10.1142/S0219720021400059 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
More links
Kategorien
Order via subito
This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.