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Open AccessArticle

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

1
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
2
Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(10), 2483; https://doi.org/10.3390/ijms20102483
Received: 5 May 2019 / Revised: 15 May 2019 / Accepted: 16 May 2019 / Published: 20 May 2019
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley)
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley. View Full-Text
Keywords: genome assembly; bread wheat; barley; optical mapping; BAC; ribosomal DNA genome assembly; bread wheat; barley; optical mapping; BAC; ribosomal DNA
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Kapustová, V.; Tulpová, Z.; Toegelová, H.; Novák, P.; Macas, J.; Karafiátová, M.; Hřibová, E.; Doležel, J.; Šimková, H. The Dark Matter of Large Cereal Genomes: Long Tandem Repeats. Int. J. Mol. Sci. 2019, 20, 2483.

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