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Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads
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SYSNO ASEP 0548344 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads Author(s) Vondrak, Tihana (BC-A) RID
Oliveira, Ludmila (BC-A) RID, ORCID
Novák, Petr (BC-A) RID, ORCID
Koblížková, Andrea (BC-A)
Neumann, Pavel (BC-A) RID, ORCID
Macas, Jiří (BC-A) RID, ORCID, SAINumber of authors 6 Source Title Computational and Structural Biotechnology Journal. - : Elsevier - ISSN 2001-0370
Roč. 19, Apr 22 (2021), s. 2179-2189Number of pages 11 s. Language eng - English Country SE - Sweden Keywords Satellite DNA ; Heterochromatin ; Oxford Nanopore sequencing ; Fluorescence in situ hybridization ; Holocentric chromosomes ; LINE elements Subject RIV EB - Genetics ; Molecular Biology OECD category Genetics and heredity (medical genetics to be 3) R&D Projects GA20-24252S GA ČR - Czech Science Foundation (CSF) LM2018131 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Research Infrastructure ELIXIR-CZ II - 90131 - Ústav organické chemie a biochemie AV ČR, v. v. i. Method of publishing Open access Institutional support BC-A - RVO:60077344 UT WOS 000684934600009 EID SCOPUS 85104729200 DOI 10.1016/j.csbj.2021.04.011 Annotation Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. Workplace Biology Centre (since 2006) Contact Dana Hypšová, eje@eje.cz, Tel.: 387 775 214 Year of Publishing 2022 Electronic address https://www.sciencedirect.com/science/article/pii/S2001037021001227?via%3Dihub
Number of the records: 1