Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants

Abstract

Gnodes is a Genome Depth Estimator for animal and plant genomes, also a genome size estimator. It calculates genome sizes based on DNA coverage of assemblies, using unique, conserved gene spans for its standard depth. Results of this tool match the independent measures from flow cytometry of genome size quite well in tests with plants and animals. Tests on a range of model and non-model animal and plant genome assemblies give reliable and accurate results, in contrast to less reliable K-mer histogram methods. The problem of half-sized assemblies of duplication-rich Daphnia is addressed. A 20-year old Arabidopsis genome discrepancy is resolved in favor of 157Mb as measured with flow-cytometry. Not all genome DNA samples contain a genome, examples and reasons for this are discussed. The T2T completed human genome assembly of 2022 is complete by Gnodes measures, with about 5% uncertainty. With full genome DNA, Gnodes measures within 10%, usually within 5%, of flow cytometry, indicating they are both measuring the same content. Public URL: http://eugenes.org/EvidentialGene/other/gnodes/

LocoGSE, a sequence-based genome size estimator for plants

“…Finally, one needs to keep in mind that k-mer based methods are very sensitive to heterozygosity ( Pucker, 2019 ) and thus need to be used cautiously. Current mapping-based approaches need to map the reads onto an assembly [ModEst ( Pfenninger et al., 2022 )] and some also necessitate a reference single copy gene set, like MGSE ( Pucker, 2019 ) and Gnodes ( Gilbert, 2022 ) for short reads, and Depthsizer ( Chen et al., 2022 ) for long reads. These approaches imply that assembly and sometimes also annotation have been performed on the genome studied, which requires high sequencing depth.…”

Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others

“…The major contents of genomes presented in these results are computed with Gnodes, as described in Gnodes#1 (Gilbert 2022). The basic algorithm of Gnodes is (a) align DNA reads to gene and chromosome assembly sequences, recording all multiple and unique map locations, (b) tabulate DNA cover depth at each sequence bin location for multiple and unique mappings, (c) measure statistical moments of coverage depth per item, itemized by categories of gene-cds, transposons and repeat annotations, duplicate and unique mappings, (d) summarize coverage and annotation tables, at chromosome-assembly and gene levels.…”

Genome assembly ofMusa beccariishows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

“…The CCS algorithm v6.0.0 ( RRID:SCR_021174 ) [ 23 ] was used to process PacBio HiFi reads and obtain consensus reads. The error-corrected short WGS reads and/or HiFi reads were used to estimate the genome size of M. beccarii via KmerGenie v1.7044 [ 24 ], GenomeScope 2.0 ( RRID:SCR_017014 ) [ 25 ], findGSE [ 26 ], GCE v1.0.2 [ 27 ], MGSE [ 28 ], and Gnodes [ 29 ]. Both MGSE and Gnodes provide mapping-based genome size estimations, while the others are k -mer based.…”