Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

BACKGROUND: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to ove...

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Autores principales: Zhu, Yunchi, Lu, Na, Chen, J.-Y., He, Chunpeng, Huang, Zhen, Lu, Zuhong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8994340/
https://www.ncbi.nlm.nih.gov/pubmed/35395709
http://dx.doi.org/10.1186/s12863-022-01038-w
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author Zhu, Yunchi
Lu, Na
Chen, J.-Y.
He, Chunpeng
Huang, Zhen
Lu, Zuhong
author_facet Zhu, Yunchi
Lu, Na
Chen, J.-Y.
He, Chunpeng
Huang, Zhen
Lu, Zuhong
author_sort Zhu, Yunchi
collection PubMed
description BACKGROUND: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. RESULTS: More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. CONCLUSIONS: Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-022-01038-w.
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spelling pubmed-89943402022-04-10 Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs Zhu, Yunchi Lu, Na Chen, J.-Y. He, Chunpeng Huang, Zhen Lu, Zuhong BMC Genom Data Research Article BACKGROUND: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. RESULTS: More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. CONCLUSIONS: Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-022-01038-w. BioMed Central 2022-04-08 /pmc/articles/PMC8994340/ /pubmed/35395709 http://dx.doi.org/10.1186/s12863-022-01038-w Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Zhu, Yunchi
Lu, Na
Chen, J.-Y.
He, Chunpeng
Huang, Zhen
Lu, Zuhong
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title_full Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title_fullStr Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title_full_unstemmed Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title_short Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs
title_sort deep whole-genome resequencing sheds light on the distribution and effect of amphioxus snps
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8994340/
https://www.ncbi.nlm.nih.gov/pubmed/35395709
http://dx.doi.org/10.1186/s12863-022-01038-w
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