Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Autoři:
Yufeng Fang aff001; Marco A. Coelho aff001; Haidong Shu aff002; Klaas Schotanus aff001; Bhagya C. Thimmappa aff003; Vikas Yadav aff001; Han Chen aff002; Ewa P. Malc aff004; Jeremy Wang aff004; Piotr A. Mieczkowski aff004; Brent Kronmiller aff005; Brett M. Tyler aff005; Kaustuv Sanyal aff003; Suomeng Dong aff002; Minou Nowrousian aff006; Joseph Heitman aff001
Působiště autorů:
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
aff001; College of Plant Protection, Nanjing Agricultural University, Nanjing, China
aff002; Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
aff003; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
aff004; Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
aff005; Lehrstuhl fuer Molekulare und Zellulaere Botanik, Ruhr-Universitaet Bochum, Bochum, Germany
aff006
Vyšlo v časopise:
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet 16(3): e32767. doi:10.1371/journal.pgen.1008646
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008646
Souhrn
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.
Klíčová slova:
Centromeres – Genomic libraries – Heterochromatin – Multiple alignment calculation – Oomycetes – Sequence alignment – Sequence assembly tools – Transposable elements
Zdroje
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