LocoGSE, a sequence-based genome size estimator for plants
Permanent lenke
https://hdl.handle.net/10037/34675Dato
2024-03-13Type
Journal articleTidsskriftartikkel
Peer reviewed
Forfatter
Guenzi-Tiberi, Pierre; Istace, Benjamin; Alsos, Inger Greve; Coissac, Eric; Lavergne, Sébastien; Aury, Jean-Marc; Denoeud, FranceSammendrag
Extensive research has focused on exploring the range of genome sizes in
eukaryotes, with a particular emphasis on land plants, where significant
variability has been observed. Accurate estimation of genome size is essential
for various research purposes, but existing sequence-based methods have
limitations, particularly for low-coverage datasets. In this study, we introduce
LocoGSE, a novel genome size estimator designed specifically for low-coverage
datasets generated by genome skimming approaches. LocoGSE relies on
mapping the reads on single copy consensus proteins without the need for a
reference genome assembly. We calibrated LocoGSE using 430 low-coverage
Angiosperm genome skimming datasets and compared its performance against
other estimators. Our results demonstrate that LocoGSE accurately predicts
monoploid genome size even at very low depth of coverage (<1X) and on highly
heterozygous samples. Additionally, LocoGSE provides stable estimates across
individuals with varying ploidy levels. LocoGSE fills a gap in sequence-based plant
genome size estimation by offering a user-friendly and reliable tool that does not
rely on high coverage or reference assemblies. We anticipate that LocoGSE will
facilitate plant genome size analysis and contribute to evolutionary and
ecological studies in the field. Furthermore, at the cost of an initial calibration,
LocoGSE can be used in other lineages.
Forlag
Frontiers MediaSitering
Guenzi-Tiberi, Istace, Alsos, Coissac, Lavergne, Aury, Denoeud. LocoGSE, a sequence-based genome size estimator for plants. Frontiers in Plant Science. 2024;15Metadata
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