Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection.
Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection.
复制标题
DOI：
10.1186/s12915-020-00899-w
复制
发表时间：
2020-11-09
期刊：
影响因子：
5.4
通讯作者：
Berriman M
中科院分区：
文献类型：
--
作者：
Olson PD;Tracey A;Baillie A;James K;Doyle SR;Buddenborg SK;Rodgers FH;Holroyd N;Berriman M
染色体水平的组装对于精确的基因预测、同线性评估和理解更高层次的基因组结构是必不可少的。主要蠕虫物种的参考和基因组草案已经出版，但对其染色体的生物学知之甚少。在这里，我们提出了完整的基因组绦虫膜壳绦虫microstoma，提供了一个参考质量，端到端的大会，代表了第一个完全组装的基因组的螺旋/lophotrochozoon，揭示了新的见解染色体进化。将长读段测序和光学作图数据添加到先前的短读段数据中，使得能够完全重新组装成六条染色体，与细胞核学一致。小的基因组大小（169 Mb）和缺乏单倍体变异（1 SNP/3.2 Mb）促成了异常高的连续性，在低复杂性序列的区域中仅剩下85个空位。重复区域的分辨率揭示了新的基因扩增，微外显子基因，和剪接的领导人反式剪接，并照亮景观的转座因子，解释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了保守的祖先连锁群，表明H。小口线虫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发挥作用，而且在保护染色体的线性完整性和全长中发挥作用。尽管经典端粒的保守性很强，但我们的研究结果表明，它们可以被更复杂的物种特异性序列所取代，如着丝粒所代表的。该组装为需要完整基因组表示的研究提供了一个强大的平台。
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.