SNP discovery using a pangenome: has the single reference approach become obsolete?

Hurgobin, Bhavna and Edwards, David (2017) SNP discovery using a pangenome: has the single reference approach become obsolete?. Biology, 6 1: . doi:10.3390/biology6010021


Author Hurgobin, Bhavna
Edwards, David
Title SNP discovery using a pangenome: has the single reference approach become obsolete?
Journal name Biology   Check publisher's open access policy
ISSN 2079-7737
Publication date 2017-03-11
Sub-type Critical review of research, literature review, critical commentary
DOI 10.3390/biology6010021
Open Access Status DOI
Volume 6
Issue 1
Total pages 12
Place of publication Basel, Switzerland
Publisher M D P I AG
Collection year 2018
Language eng
Abstract Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species, it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation. The advent of next-generation sequencing (NGS) coupled with the heritability of SNPs make them ideal markers for genetic analysis of human, animal, and microbial data. SNPs have also been extensively used in crop genetics for association mapping, quantitative trait loci (QTL) analysis, analysis of genetic diversity, and phylogenetic analysis. This review focuses on the use of pangenomes for SNP discovery. It highlights the advantages of using a pangenome rather than a single reference for this purpose. This review also demonstrates how extra information not captured in a single reference alone can be used to provide additional support for linking genotypic data to phenotypic data.
Keyword Assembly
Copy number variation
Core genome
Gene
Genetic diversity
Pangenome
Presence absence variation
Single nucleotide polymorphism
SNP discovery
Variable genome
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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