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

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.

着丝粒（centromeres）是一类染色体区域，可作为动粒（kinetochore）组装与纺锤体附着的平台，保障细胞分裂过程中染色体的精准分离。尽管功能上具有保守性，着丝粒的DNA序列却呈现多样性且常为重复序列，这使得其组装与鉴定颇具挑战。本研究结合基于长读长测序的基因组组装技术，以及针对着丝粒组蛋白CENP-A的染色质免疫共沉淀结合高通量测序（ChIP-seq），解析了卵菌（oomycete）大豆疫霉菌（Phytophthora sojae）中的着丝粒。大豆疫霉菌的着丝粒在不同生命阶段以及核分裂过程中，均聚集于单个焦点处。本研究报道了大豆疫霉菌参考菌株的优化版基因组组装结果，借此鉴定出15个富集CENP-A结合的区域作为潜在着丝粒。通过聚焦其中部分区域，我们证实大豆疫霉菌的着丝粒为区域型着丝粒，跨度介于211 kb至356 kb之间。此类区域大多富含转座子、转录水平较低，且缺乏组蛋白修饰H3K4me2，但嵌入在带有异染色质标记H3K9me3和H3K27me3的区域内。值得注意的是，我们发现了一类在CENP-A染色质中高度富集的类Copia转座子（CoLT）。类似的聚集元件在大豆疫霉菌的卵菌近缘物种中也有存在，或可作为预测卵菌着丝粒的判定标准。相较于SAR超类群（Stramenopila-Alveolata-Rhizaria）中的其他生物——包括拥有相对短小简单的区域型着丝粒的硅藻和恶性疟原虫（Plasmodium falciparum）——本研究揭示了卵菌中着丝粒特征的分化。对大豆疫霉菌着丝粒的鉴定，同时也推动了其基因组组装的完善。