The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

0506096 - ÚEB 2020 RIV CH eng J - Článek v odborném periodiku
Kapustová, Veronika - Tulpová, Zuzana - Toegelová, Helena - Novák, Petr - Macas, Jiří - Karafiátová, Miroslava - Hřibová, Eva - Doležel, Jaroslav - Šimková, Hana
The Dark Matter of Large Cereal Genomes: Long Tandem Repeats.
International Journal of Molecular Sciences. Roč. 20, č. 10 (2019), č. článku 2483. E-ISSN 1422-0067
Grant CEP: GA ČR(CZ) GA17-17564S; GA MŠMT(CZ) EF16_019/0000827
Institucionální podpora: RVO:61389030 ; RVO:60077344
Klíčová slova: bac * barley * bread wheat * genome assembly * optical mapping * ribosomal DNA
Obor OECD: Biochemistry and molecular biology; Genetics and heredity (medical genetics to be 3) (BC-A)
Impakt faktor: 4.556, rok: 2019
Způsob publikování: Open access
http://doi.org/10.3390/ijms20102483

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.
Trvalý link: http://hdl.handle.net/11104/0297367