Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

Abstract Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12)...

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Autores principales:	Laura Ávila Robledillo, Andrea Koblížková, Petr Novák, Katharina Böttinger, Iva Vrbová, Pavel Neumann, Ingo Schubert, Jiří Macas
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/52faa5df29b84f10a64a77264fd390b3
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spelling	oai:doaj.org-article:52faa5df29b84f10a64a77264fd390b32021-12-02T15:07:50ZSatellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing10.1038/s41598-018-24196-32045-2322https://doaj.org/article/52faa5df29b84f10a64a77264fd390b32018-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-24196-3https://doaj.org/toc/2045-2322Abstract Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.Laura Ávila RobledilloAndrea KoblížkováPetr NovákKatharina BöttingerIva VrbováPavel NeumannIngo SchubertJiří MacasNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Laura Ávila Robledillo Andrea Koblížková Petr Novák Katharina Böttinger Iva Vrbová Pavel Neumann Ingo Schubert Jiří Macas Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
description	Abstract Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.
format	article
author	Laura Ávila Robledillo Andrea Koblížková Petr Novák Katharina Böttinger Iva Vrbová Pavel Neumann Ingo Schubert Jiří Macas
author_facet	Laura Ávila Robledillo Andrea Koblížková Petr Novák Katharina Böttinger Iva Vrbová Pavel Neumann Ingo Schubert Jiří Macas
author_sort	Laura Ávila Robledillo
title	Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
title_short	Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
title_full	Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
title_fullStr	Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
title_full_unstemmed	Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
title_sort	satellite dna in vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/52faa5df29b84f10a64a77264fd390b3
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Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

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