![]() Nevertheless, studies following best practices and using internal reference standards have revealed genome size variation in numerous species ( Achigan-Dako et al., 2008 Šmarda et al., 2010 Díez et al., 2013 Hanušová et al., 2014 Blommaert, 2020).īetween the species of embryophyte plants, genome size shows a staggering 2400-fold variation ( Pellicer et al., 2018). However, the magnitude of this variation and whether it can be detected by methods such as microdensitometry or flow cytometry has been subject to debate, and some older reports have been refuted ( Greilhuber, 2005 Suda and Leitch, 2010). ![]() Because of the ubiquity in populations of structural genomic variation such as ploidy differences, supernumerary chromosomes, segmental duplications, and other ‘indels’, the assumption of intraspecific genome size variation should be the norm. E.g., a deletion of a part of the genome causes a smaller genome size. ![]() Genome size is a trait immediately shaped by structural genomic variation. As recent and ongoing advances in DNA sequencing technology have revolutionised the community’s ability to characterise the genetic variation on the sequence level, it is now possible to study, at unprecedented detail, the sequences underpinning genome size variation within and between closely related species. These are all associated with structural genomic variation, genomic repeats, and they contribute to genome size variation. Creighton and McClintock, 1931), heterochromatin ( Heitz, 1928), and B chromosomes ( Jones, 1995 and references therein). Over the past century, cytogeneticists have uncovered various genomic phenomena such as repetitive neocentromers ‘knobs’ (e.g. To allow future work with other taxonomic groups, we share our analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools. We also show that studies of genome size variation should go beyond repeats and consider the whole genome. Such sequences can serve as targets for future cytogenetic studies. In this study, we demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without use of a reference genome. We also find size differences in the low-copy number class, likely indicating differences in gene space between our samples. While all copy number classes contributed to genome size variation, the largest contribution came from repeats with 1000-10,000 genomic copies including the 45S rDNA satellite DNA and, unexpectedly, a repeat associated with an Angela transposable element. We find complex patterns of k-mer differences between samples. We further assign high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole genome sequencing data of diploid eyebrights ( Euphrasia), a group of plants which have considerable genome size variation within a ploidy level. However, identifying the sequences underpinning genome size variation has been challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies miss low-copy number sequences. Genome size variation within plant (and other) taxa may be due to presence/absence variation in low-copy sequences or copy number variation in genomic repeats of various frequency classes.
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