#Rapidcopy copy if idfferent size dat full

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 of structural genomic variation in populations, including ploidy differences, supernumerary chromosomes, segmental duplications and other ‘indels’, the assumption of intraspecific genome size variation is a plausible null hypothesis. For example, a deletion of a part of the genome results in a smaller genome size. Genome size is a trait directly affected by structural genomic variation. As recent and ongoing advances in DNA sequencing technology have revolutionised the community’s ability to characterise genetic variation at 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 and genomic repeats, which, in turn, contribute to genome size variation. Over the past century, cytogenetics researchers have uncovered various genomic features such as repetitive neocentromers ‘knobs’ (e.g., Creighton and McClintock, 1931), heterochromatin ( Heitz, 1928) and B chromosomes ( Jones, 1995 and references therein). To allow future work with other taxonomic groups, we share our k-mer analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

#Rapidcopy copy if idfferent size dat full

We also show that studies of genome size variation should go beyond repeats if they aim to characterise the full range of genomic variants. Such sequences can serve as targets for future cytogenetic studies. We demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without the use of a reference genome. We also find size differences in the low-copy number class (copy number ≤ 10×) of up to 27 Mbp, possibly indicating differences in gene space between our samples. The largest contributions to these differences come from rDNA sequences, a 145-nt genomic satellite and a repeat associated with an Angela transposable element. We find genome size differences of up to 230Mbp, equivalent to more than 20% genome size variation. We further match 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 that have considerable genome size variation within a ploidy level. However, identifying the sequences underpinning genome size variation is challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies by design miss low-copy number sequences. Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes.

2Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom.1School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.Hannes Becher 1 *, Jacob Sampson 1 and Alex D.