iLoci: Robust evaluation of genome content and organization for provisional and mature genome assemblies [article]

Daniel S Standage, Tim Lai, Volker P Brendel
2021 bioRxiv   pre-print
AbstractBackgroundThe rate at which new draft genome assemblies and corresponding annotation versions are being produced has long outpaced the scientific community's capacity to refine these drafts into "finished," reference-quality data resources to a standard typically expected from dedicated efforts of model organism research communities. Nonetheless, scientists must be able to evaluate newly sequenced genomes in the context of previously published data, requiring summaries of genome content
more » ... and organization that can be quickly computed, updated, and meaningfully compared. As annotation quality will necessarily vary within and across data sets, the ability to select subsets of only those data that are well supported is critical for distinguishing technical artifacts from biological effects in genome-wide analyses.ResultsWe introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide characteristics of gene arrangements in the whole genome context.ConclusionsWe present a coherent computational framework that calculates informative statistics from genome assembly/annotation data input. Given the fast pace of assembly/annotation updates, our AEGeAn Toolkit fills a niche in computational genomics based on deriving persistent and species-specific genome statistics. Gene structure model centric iLoci provide a precisely defined coordinate system that can be used to store assembly/annotation updates that reflect either stable or changed assessments. Large-scale application of the approach revealed species and clade specific genome organization in precisely defined computational terms, promising intriguing forays into the forces of shaping genome structure as more and more genome assemblies are being deposited.
doi:10.1101/2021.10.03.462917 fatcat:lg6ru2er6fbuxjciarpykkygsy