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Centromere evolution and CpG methylation during vertebrate speciation

Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-...

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Autores principales: Ichikawa, Kazuki, Tomioka, Shingo, Suzuki, Yuta, Nakamura, Ryohei, Doi, Koichiro, Yoshimura, Jun, Kumagai, Masahiko, Inoue, Yusuke, Uchida, Yui, Irie, Naoki, Takeda, Hiroyuki, Morishita, Shinich
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705604/
https://www.ncbi.nlm.nih.gov/pubmed/29184138
http://dx.doi.org/10.1038/s41467-017-01982-7
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author Ichikawa, Kazuki
Tomioka, Shingo
Suzuki, Yuta
Nakamura, Ryohei
Doi, Koichiro
Yoshimura, Jun
Kumagai, Masahiko
Inoue, Yusuke
Uchida, Yui
Irie, Naoki
Takeda, Hiroyuki
Morishita, Shinich
author_facet Ichikawa, Kazuki
Tomioka, Shingo
Suzuki, Yuta
Nakamura, Ryohei
Doi, Koichiro
Yoshimura, Jun
Kumagai, Masahiko
Inoue, Yusuke
Uchida, Yui
Irie, Naoki
Takeda, Hiroyuki
Morishita, Shinich
author_sort Ichikawa, Kazuki
collection PubMed
description Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
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spelling pubmed-57056042017-12-02 Centromere evolution and CpG methylation during vertebrate speciation Ichikawa, Kazuki Tomioka, Shingo Suzuki, Yuta Nakamura, Ryohei Doi, Koichiro Yoshimura, Jun Kumagai, Masahiko Inoue, Yusuke Uchida, Yui Irie, Naoki Takeda, Hiroyuki Morishita, Shinich Nat Commun Article Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation. Nature Publishing Group UK 2017-11-28 /pmc/articles/PMC5705604/ /pubmed/29184138 http://dx.doi.org/10.1038/s41467-017-01982-7 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commonslicense, unless indicated otherwise in a credit line to the material. If material is not included in the article’sCreative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ichikawa, Kazuki
Tomioka, Shingo
Suzuki, Yuta
Nakamura, Ryohei
Doi, Koichiro
Yoshimura, Jun
Kumagai, Masahiko
Inoue, Yusuke
Uchida, Yui
Irie, Naoki
Takeda, Hiroyuki
Morishita, Shinich
Centromere evolution and CpG methylation during vertebrate speciation
title Centromere evolution and CpG methylation during vertebrate speciation
title_full Centromere evolution and CpG methylation during vertebrate speciation
title_fullStr Centromere evolution and CpG methylation during vertebrate speciation
title_full_unstemmed Centromere evolution and CpG methylation during vertebrate speciation
title_short Centromere evolution and CpG methylation during vertebrate speciation
title_sort centromere evolution and cpg methylation during vertebrate speciation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705604/
https://www.ncbi.nlm.nih.gov/pubmed/29184138
http://dx.doi.org/10.1038/s41467-017-01982-7
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