Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F20%3A43901373" target="_blank" >RIV/60076658:12310/20:43901373 - isvavai.cz</a>
Alternative codes found
RIV/60077344:_____/20:00532438
Result on the web
<a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.14546" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1111/tpj.14546</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/tpj.14546" target="_blank" >10.1111/tpj.14546</a>
Alternative languages
Result language
angličtina
Original language name
Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats
Original language description
Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
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
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Plant Journal
ISSN
0960-7412
e-ISSN
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Volume of the periodical
101
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
17
Pages from-to
484-500
UT code for WoS article
000509498700016
EID of the result in the Scopus database
2-s2.0-85074817733