The centromere DNA locus on a eukaryotic chromosome facilitates faithful chromosome segregation. Despite performing such a conserved function, centromere DNA sequence as well as the organization of sequence elements is rapidly evolving in all forms of eukaryotes. The driving force that facilitates centromere evolution remains an enigma. Here, we studied the evolution of centromeres in closely related species in the fungal phylum of Basidiomycota. Using ChIP-seq analysis of conserved inner kinetochore proteins, we identified centromeres in three closely related Cryptococcus species: two of which are RNAi-proficient, while the other lost functional RNAi. We find that the centromeres in the RNAi-deficient species are significantly shorter than those of the two RNAi-proficient species. While centromeres are LTR retrotransposon-rich in all cases, the RNAi-deficient species lost all full-length retroelements from its centromeres. In addition, centromeres in RNAi-proficient species are associated with a significantly higher level of cytosine DNA modifications compared with those of RNAi-deficient species. Furthermore, when an RNAi-proficient Cryptococcus species and its RNAi-deficient mutants were passaged under similar conditions, the centromere length was found to be occasionally shortened in RNAi mutants. In silico analysis of predicted centromeres in a group of closely related Ustilago species, also belonging to the Basidiomycota, were found to have undergone a similar transition in the centromere length in an RNAi-dependent fashion. Based on the correlation found in two independent basidiomycetous species complexes, we present evidence suggesting that the loss of RNAi and cytosine DNA methylation triggered transposon attrition, which resulted in shortening of centromere length during evolution.

真核染色体上的着丝粒DNA基因座有助于忠实的染色体分离。尽管执行这种保守功能，着丝粒DNA序列以及序列元件的组织在所有形式的真核生物中迅速发展。促进着丝粒进化的驱动力仍然是一个谜。在这里，我们研究了担子菌真菌门中紧密相关物种中着丝粒的进化。使用保守内动粒蛋白的ChIP-seq分析，我们在三个密切相关的隐球菌中鉴定了着丝粒物种：其中两个是RNAi熟练的，而另一个则失去了功能性RNAi。我们发现，RNAi缺陷物种中的着丝粒比两个RNAi缺陷物种中的着丝粒短得多。尽管在所有情况下着丝粒都富含LTR反转录转座子，但RNAi缺陷型物种却失去了着丝粒的所有全长反转录元件。此外，与RNAi缺陷物种相比，RNAi优势物种中的着丝粒与胞嘧啶DNA修饰水平显着更高。此外，当在相似的条件下传代RNAi优势的隐球菌种及其RNAi缺陷的突变体时，发现RNAi突变体的着丝粒长度有时会缩短。对一组密切相关的预测着丝粒进行计算机分析发现乌斯梯亚戈属菌也属于担子菌属，其着丝粒长度以RNAi依赖性方式经历了类似的转变。基于在两个独立的担子菌物种复合物中发现的相关性，我们目前的证据表明RNAi和胞嘧啶DNA甲基化的丧失触发了转座子的损耗，从而导致进化过程中着丝粒长度的缩短。