Abstract
BackgroundDispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups.ResultsHere, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.ConclusionsInstead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.
Highlights
Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level
Calculation of gene dispensability scores–QUantification Of gene Dispensability (QUOD) QUOD calculates a reference-based gene dispensability score for each structurally annotated gene based on supplied mapping files (BAM) and a structural annotation of the reference sequence (GFF)
In this study, a bioinformatic tool was developed to calculate a gene-specific dispensability score based on the normalised coverage in a read mapping
Summary
Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Genetic variation is not restricted to single nucleotide polymorphisms or small insertions and deletions but extends to (large) structural variations These structural variations include copy number variations (CNVs) and presence/absence variations (PAVs), which can cause substantial variation of the gene content among individual genomes [1, 2]. A third category of ‘conditionally dispensable’ genes is invoked [12] or genes might be classified as ‘cloud’, ‘shell’, ‘softcore’ and ‘core’ [13] or even as ‘core’, ‘softcore’, ‘dispensable’ and ‘private’ [14] This distinct classification is not based on the biological dispensability of genes and relies on one or multiple arbitrary cutoffs. One way to circumvent this is to rely only on high-quality reference genome sequences, avoiding additional assemblies which are potential sources of errors
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
