Počet záznamů: 1
Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats
- 1.0532438 - BC 2021 RIV GB eng J - Článek v odborném periodiku
Vondrak, Tihana - Robledillo, Laura Avila - Novák, Petr - Koblížková, Andrea - Neumann, Pavel - Macas, Jiří
Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats.
Plant Journal. Roč. 101, č. 2 (2020), s. 484-500. ISSN 0960-7412. E-ISSN 1365-313X
Grant CEP: GA MŠMT(CZ) LM2015047; GA MŠMT(CZ) EF16_013/0001777
Institucionální podpora: RVO:60077344
Klíčová slova: nanopore sequencing * centromeres * heterochromatin * fluorescence in situ hybridization (FISH) * technical advance
Obor OECD: Genetics and heredity (medical genetics to be 3)
Impakt faktor: 6.486, rok: 2020
Způsob publikování: Open access
https://onlinelibrary.wiley.com/doi/10.1111/tpj.14546
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.
Trvalý link: http://hdl.handle.net/11104/0310931
Počet záznamů: 1