Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation.

中文翻译：

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绦虫基因组的完整表示揭示了染色体被着丝粒覆盖，需要在隔离和保护中发挥双重作用

染色体水平的组装对于准确的基因预测、同线性评估和理解高阶基因组结构是必不可少的。主要蠕虫物种的参考基因组和草图已经发表，但对其染色体的生物学知之甚少。在这里，我们展示了绦虫 Hymenolepis microstoma 的完整基因组，提供了参考质量的端到端组装，它代表了螺旋线虫 / 活轮虫的第一个完全组装的基因组，揭示了对染色体进化的新见解。长读长测序和光学映射数据被添加到之前的短读数据中，能够完全重新组装成六条染色体，与核学一致。小基因组大小 (169 Mb) 和缺乏单倍体变异 (1 SNP/3. 2 Mb) 促成了极高的连续性，在低复杂性序列的区域中仅剩下 85 个缺口。重复区域的解析揭示了新的基因扩展、微外显子基因和剪接前导反式剪接，并阐明了转座元件的景观，解释了观察到的姐妹染色单体的长度差异。与其他寄生扁虫的同线比较显示保守的祖先连锁群表明 H. microstoma 核型通过融合事件进化。引人注目的是，该组装揭示了染色体终止于着丝粒阵列，表明这些基序不仅在分离中起作用，而且在保护染色体的线性完整性和全长方面也起作用。尽管规范端粒具有很强的保守性，但我们的结果表明它们可以被更复杂的、物种特异性序列，由着丝粒表示。该程序集为需要完整基因组表示的研究提供了一个强大的平台。