Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.
Alveolata
/ genetics
Centromere
/ genetics
Centromere Protein A
/ genetics
Chromatin
/ genetics
Chromatin Immunoprecipitation
/ methods
Chromosomal Proteins, Non-Histone
/ genetics
Chromosome Segregation
/ genetics
Heterochromatin
/ genetics
Histones
/ genetics
Kinetochores
/ metabolism
Oomycetes
/ genetics
Phytophthora
/ genetics
Rhizaria
/ genetics
Stramenopiles
/ genetics
Journal
PLoS genetics
ISSN: 1553-7404
Titre abrégé: PLoS Genet
Pays: United States
ID NLM: 101239074
Informations de publication
Date de publication:
03 2020
03 2020
Historique:
received:
03
10
2019
accepted:
03
02
2020
revised:
19
03
2020
pubmed:
10
3
2020
medline:
22
7
2020
entrez:
10
3
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32150559
doi: 10.1371/journal.pgen.1008646
pii: PGENETICS-D-19-01652
pmc: PMC7082073
doi:
Substances chimiques
Centromere Protein A
0
Chromatin
0
Chromosomal Proteins, Non-Histone
0
Heterochromatin
0
Histones
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1008646Subventions
Organisme : NIAID NIH HHS
ID : R01 AI039115
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI050113
Pays : United States
Organisme : NIAID NIH HHS
ID : R37 AI039115
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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