A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
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DOI：
10.1101/gr.199448.115
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发表时间：
2016-04
期刊：
影响因子：
7
通讯作者：
Makova KD
中科院分区：
文献类型：
--
作者：
Tomaszkiewicz M;Rangavittal S;Cechova M;Campos Sanchez R;Fescemyer HW;Harris R;Ye D;O'Brien PC;Chikhi R;Ryder OA;Ferguson-Smith MA;Medvedev P;Makova KD
哺乳动物的Y染色体序列对研究男性的生育和扩散至关重要，它富含重复和回文，因此是基因组中最难组装的组成部分。以前，昂贵和劳动密集型的基于BAC的技术被用于少数哺乳动物物种的Y序列测定。在这里，我们提出了一种更快、更实惠的策略，用于为大多数比较基因组学分析和保护遗传学应用提供足够质量的哺乳动物Y染色体测序和组装。该策略将流动排序、短和长阅读基因组和转录组测序、液滴数字聚合酶链式反应与新的和现有的计算方法相结合。它可以用来重建任何物种的异性配子的性染色体。我们应用我们的策略产生了大猩猩Y序列的草稿。由此产生的组装使我们能够提炼基因内容，评估扩增基因家族的拷贝数，定位特定物种的回文，检查重复元素的含量，并产生与人类和黑猩猩Y染色体的序列比对。我们的结果为人类(人、黑猩猩和大猩猩)Y染色体的进化提供了信息。令人惊讶的是，我们发现大猩猩的Y染色体与人类的Y染色体相似，但与黑猩猩的Y染色体不同。此外，我们还利用组装的大猩猩Y染色体序列设计了遗传标记，以研究这种濒危物种的雄性特有的扩散。
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.