The selection of reference genome and the search for the origin of SARS-CoV-2
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The pandemic caused by SARS-CoV-2 has a great impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins were considered a potential intermediate host. To assemble the coronavirus found in pangolins, SARS-CoV-2 were used a reference genome in most of studies, assuming that pangolins CoV and SARS-CoV-2 are the closest neighbors in the evolution. However, this assumption may not be true. We investigated how the selection of reference genome affect the resulting CoV genome assembly. We explored various representative CoV as reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts.
Article activity feed
-
SciScore for 10.1101/2020.08.10.245290: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data selection: Two RNA-seq samples, lung07 and lung08, were downloaded from NCBI SRA under BioProject SRA: PRJNA573298. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)To eliminate host contamination, the remaining reads were aligned to the Manis javanica genome (SRA: PRJNA256023) using BWA-aln (version 0.7.17) [6] and reads mapped to the host genome were discarded. BWA-alnsuggested: NoneOnce a reference genome was picked, the cleaned reads were aligned to the reference … SciScore for 10.1101/2020.08.10.245290: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data selection: Two RNA-seq samples, lung07 and lung08, were downloaded from NCBI SRA under BioProject SRA: PRJNA573298. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)To eliminate host contamination, the remaining reads were aligned to the Manis javanica genome (SRA: PRJNA256023) using BWA-aln (version 0.7.17) [6] and reads mapped to the host genome were discarded. BWA-alnsuggested: NoneOnce a reference genome was picked, the cleaned reads were aligned to the reference genome using BWA-MEM [5], and the mapped reads were assembled de novo using MEGHIT (version 1.1.3) with meta-sensitive mode [4]. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)MEGHITsuggested: NonePhylogenetic and similarity analyses: Phylogenetic distance analysis was performed using MEGA X (version 10.1.8) [2]. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)The whole genome nucleotide identity analysis was performed in SimPlot 3.5.1 [10]. SimPlotsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
-
SciScore for 10.1101/2020.08.10.245290: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Pangolins-CoV obtained from the Guangdong collection and the Guangxi collection represent two lineages of coronavirus [3]. Pangolins-CoVsuggested: NoneSoftware and Algorithms Sentences Resources To eliminate host contamination, the remaining reads were aligned to the Manis javanica genome (SRA: PRJNA256023) using BWAaln (version 0.7.17) [6] and reads … SciScore for 10.1101/2020.08.10.245290: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Pangolins-CoV obtained from the Guangdong collection and the Guangxi collection represent two lineages of coronavirus [3]. Pangolins-CoVsuggested: NoneSoftware and Algorithms Sentences Resources To eliminate host contamination, the remaining reads were aligned to the Manis javanica genome (SRA: PRJNA256023) using BWAaln (version 0.7.17) [6] and reads mapped to the host genome were discarded. BWAalnsuggested: NoneOnce a reference genome was picked, the cleaned reads were aligned to the reference genome using BWA-MEM [5], and the mapped reads were assembled de novo using MEGHIT BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)MEGHITsuggested: NonePhylogenetic and similarity analyses Phylogenetic distance analysis was performed using MEGA X (version 10.1.8) [2]. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)The whole genome nucleotide identity analysis was performed in SimPlot 3.5.1 [10] SimPlotsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
-
