Reference-based QUantification Of gene Dispensability (QUOD)

BioRxiv : the Preprint Server for Biology
K. SielemannB. Pucker

Abstract

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. 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. Here, 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...Continue Reading

Related Concepts

Electroencephalography
Trees (plant)
Nerve Degeneration
Motor Neurons
Amyotrophic Lateral Sclerosis
Lower Motor Neuron
Neuroimaging
Monitoring - Action
Analysis
Interphase Cell

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

ALS

Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is associated with the death of neurons that control voluntary muscles. Discover the latest research on ALS here.