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Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.

Publication ,  Journal Article
Fang, Y; Coelho, MA; Shu, H; Schotanus, K; Thimmappa, BC; Yadav, V; Chen, H; Malc, EP; Wang, J; Mieczkowski, PA; Kronmiller, B; Tyler, BM ...
Published in: PLoS Genet
March 2020

Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often repetitive, making them challenging to assemble and identify. Here, we describe centromeres in an oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and during nuclear division. We report an improved genome assembly of the P. sojae reference strain, which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the histone modification H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup including diatoms and Plasmodium falciparum that have relatively short and simple regional centromeres. Identification of P. sojae centromeres in turn also advances the genome assembly.

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Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

March 2020

Volume

16

Issue

3

Start / End Page

e1008646

Location

United States

Related Subject Headings

  • Stramenopiles
  • Rhizaria
  • Phytophthora
  • Oomycetes
  • Kinetochores
  • Histones
  • Heterochromatin
  • Developmental Biology
  • Chromosome Segregation
  • Chromosomal Proteins, Non-Histone
 

Citation

APA
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MLA
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Fang, Y., Coelho, M. A., Shu, H., Schotanus, K., Thimmappa, B. C., Yadav, V., … Heitman, J. (2020). Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet, 16(3), e1008646. https://doi.org/10.1371/journal.pgen.1008646
Fang, Yufeng, Marco A. Coelho, Haidong Shu, Klaas Schotanus, Bhagya C. Thimmappa, Vikas Yadav, Han Chen, et al. “Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.PLoS Genet 16, no. 3 (March 2020): e1008646. https://doi.org/10.1371/journal.pgen.1008646.
Fang Y, Coelho MA, Shu H, Schotanus K, Thimmappa BC, Yadav V, et al. Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet. 2020 Mar;16(3):e1008646.
Fang, Yufeng, et al. “Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.PLoS Genet, vol. 16, no. 3, Mar. 2020, p. e1008646. Pubmed, doi:10.1371/journal.pgen.1008646.
Fang Y, Coelho MA, Shu H, Schotanus K, Thimmappa BC, Yadav V, Chen H, Malc EP, Wang J, Mieczkowski PA, Kronmiller B, Tyler BM, Sanyal K, Dong S, Nowrousian M, Heitman J. Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet. 2020 Mar;16(3):e1008646.

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

March 2020

Volume

16

Issue

3

Start / End Page

e1008646

Location

United States

Related Subject Headings

  • Stramenopiles
  • Rhizaria
  • Phytophthora
  • Oomycetes
  • Kinetochores
  • Histones
  • Heterochromatin
  • Developmental Biology
  • Chromosome Segregation
  • Chromosomal Proteins, Non-Histone