The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F19%3A00506096" target="_blank" >RIV/61389030:_____/19:00506096 - isvavai.cz</a>
Alternative codes found
RIV/60077344:_____/19:00506096
Result on the web
<a href="http://doi.org/10.3390/ijms20102483" target="_blank" >http://doi.org/10.3390/ijms20102483</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/ijms20102483" target="_blank" >10.3390/ijms20102483</a>
Alternative languages
Result language
angličtina
Original language name
The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
International Journal of Molecular Sciences
ISSN
1422-0067
e-ISSN
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Volume of the periodical
20
Issue of the periodical within the volume
10
Country of publishing house
CH - SWITZERLAND
Number of pages
12
Pages from-to
2483
UT code for WoS article
000471001400114
EID of the result in the Scopus database
2-s2.0-85067311944