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Chrisman BS, Paskov K, Stockham N, Tabatabaei K, Jung JY, Washington P, Varma M, Sun MW, Maleki S, Wall DP. Indels in SARS-CoV-2 occur at template-switching hotspots. BioData Min 2021; 14:20. [PMID: 33743803 PMCID: PMC7980745 DOI: 10.1186/s13040-021-00251-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022] Open
Abstract
The evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ignored the role of insertions and deletions (indels) as well as recombination in SARS-CoV-2 evolution. Using sequences from the GISAID database, we catalogue over 100 insertions and deletions in the SARS-CoV-2 consensus sequences. We hypothesize that these indels are artifacts of recombination events between SARS-CoV-2 replicates whereby RNA-dependent RNA polymerase (RdRp) re-associates with a homologous template at a different loci ("imperfect homologous recombination"). We provide several independent pieces of evidence that suggest this. (1) The indels from the GISAID consensus sequences are clustered at specific regions of the genome. (2) These regions are also enriched for 5' and 3' breakpoints in the transcription regulatory site (TRS) independent transcriptome, presumably sites of RNA-dependent RNA polymerase (RdRp) template-switching. (3) Within raw reads, these indel hotspots have cases of both high intra-host heterogeneity and intra-host homogeneity, suggesting that these indels are both consequences of de novo recombination events within a host and artifacts of previous recombination. We briefly analyze the indels in the context of RNA secondary structure, noting that indels preferentially occur in "arms" and loop structures of the predicted folded RNA, suggesting that secondary structure may be a mechanism for TRS-independent template-switching in SARS-CoV-2 or other coronaviruses. These insights into the relationship between structural variation and recombination in SARS-CoV-2 can improve our reconstructions of the SARS-CoV-2 evolutionary history as well as our understanding of the process of RdRp template-switching in RNA viruses.
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Affiliation(s)
| | - Kelley Paskov
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Nate Stockham
- Department of Neuroscience, Stanford University, Stanford, USA
| | - Kevin Tabatabaei
- Faculty of Health Sciences, McMaster University, Hamilton, Canada
| | - Jae-Yoon Jung
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Maya Varma
- Department of Computer Science, Stanford University, Stanford, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Sepideh Maleki
- Department of Computer Science, University of Texas Austin, Austin, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Stanford University, Stanford, USA.
- Department of Pediatrics (Systems Medicine), Stanford University, Stanford, USA.
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Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs. Sci Rep 2016; 6:27534. [PMID: 27270507 PMCID: PMC4897638 DOI: 10.1038/srep27534] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
A common phenotypic difference among domestic animals is variation in coat color. Six-white-point is a pigmentation pattern observed in varying pig breeds, which seems to have evolved through several different mechanistic pathways. Herein, we re-sequenced whole genomes of 31 Diannan small-ear pigs from China and found that the six-white-point coat color in Diannan small-ear pigs is likely regulated by polygenic loci, rather than by the MC1R locus. Strong associations were observed at three loci (EDNRB, CNTLN, and PINK1), which explain about 20 percent of the total coat color variance in the Diannan small-ear pigs. We found a mutation that is highly differentiated between six-white-point and black Diannan small-ear pigs, which is located in a conserved noncoding sequence upstream of the EDNRB gene and is a putative binding site of the CEBPB protein. This study advances our understanding of coat color evolution in Diannan small-ear pigs and expands our traditional knowledge of coat color being a monogenic trait.
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