Long-read sequence assembly: A technical evaluation in barley
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F21%3A00549408" target="_blank" >RIV/61389030:_____/21:00549408 - isvavai.cz</a>
Result on the web
<a href="http://doi.org/10.1093/plcell/koab077" target="_blank" >http://doi.org/10.1093/plcell/koab077</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/plcell/koab077" target="_blank" >10.1093/plcell/koab077</a>
Alternative languages
Result language
angličtina
Original language name
Long-read sequence assembly: A technical evaluation in barley
Original language description
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
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
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Plant Cell
ISSN
1040-4651
e-ISSN
1532-298X
Volume of the periodical
33
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
19
Pages from-to
1888-1906
UT code for WoS article
000685239200009
EID of the result in the Scopus database
2-s2.0-85107430461