Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Apr 8;23(1):26.
doi: 10.1186/s12863-022-01038-w.

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

Yunchi Zhu #  1 , Na Lu #  1 , J-Y Chen  2 , Chunpeng He  3 , Zhen Huang  4   5 , Zuhong Lu  6
Affiliations

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

Yunchi Zhu et al. BMC Genom Data. .

Abstract

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.

Keywords: AlphaFold2; Amphioxus; SNP; Whole-genome resequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Distribution and effect of B. belcheri SNPs. a SNP distribution in B. belcheri chromosomes. Each portion of chromosome is 1 Mbp. b Statistics of SNPs detected in each type of genomic region. c Statistics of SNPs causing each variant type. Variant types are described by Sequence Ontology terms
Fig. 2
Fig. 2
GO enrichment results of top-1000 genes with largest number of intron variants, synonymous variants, and missense variants. Enrichment plots are generated with categories marked by colour and statistical significance (PPDE = 1 – P value) marked by transparency. PPDE legend displays the gradient of transparency
Fig. 3
Fig. 3
Results of pN/pS analysis. a Distribution of pN/pS ratios of genes with a minimum of five synonymous SNPs. b KEGG enrichment results of genes with pN/pS > 1.5. KEGG.M, KEGG.CP, KEGG.EIP, KEGG.OS are short for metabolism, cellular processes, environmental information processing and organismal systems in KEGG. Enrichment plots are generated with categories marked by colour and statistical significance (PPDE = 1 – P value) marked by transparency. PPDE legend displays the gradient of transparency
Fig. 4
Fig. 4
Examples of protein structure variation brought by SNPs. For each example, raw SNP-absent structure is marked by green and SNP-present structure is marked by blue. SNPs are located in the red-squared regions. Structures with SNPs are aligned to original structures for comparison, where overlapping green–blue regions can be recognized as unchanged
See this image and copyright information in PMC

References

    1. Holland LZ, Albalat R, Azumi K, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008;18(7):1100–1111. doi: 10.1101/gr.073676.107. - DOI - PMC - PubMed
    1. Putnam NH, Butts T, Ferrier DE, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008;453(7198):1064–1071. doi: 10.1038/nature06967. - DOI - PubMed
    1. Huang S, Chen Z, Yan X, et al. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun. 2014;5(1):5896. doi: 10.1038/ncomms6896. - DOI - PMC - PubMed
    1. Marlétaz F, Firbas PN, Maeso I, et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018;564(7734):64–70. doi: 10.1038/s41586-018-0734-6. - DOI - PMC - PubMed
    1. Yuan S, Ruan J, Huang S, Chen S, Xu A. Amphioxus as a model for investigating evolution of the vertebrate immune system. Dev Comp Immunol. 2015;48(2):297–305. doi: 10.1016/j.dci.2014.05.004. - DOI - PubMed

Publication types