Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome
Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome
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DOI：
10.1534/genetics.118.301765
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发表时间：
2019-01-01
期刊：
影响因子：
3.3
通讯作者：
Larracuente, Amanda M.
中科院分区：
文献类型：
--
作者：
Chang, Ching-Ho;Larracuente, Amanda M.
基因组的异染色质区域重复丰富，但蛋白质编码基因贫乏，因此即使在最好的基因组组装中，其代表性也不足。基因组中最难组装的区域之一是限性染色体。果蝇 Y 染色体完全是异染色质，但对雄性生育力、健康和全基因组基因表达具有广泛影响。这种表型变异的遗传基础很难研究，部分原因是我们不知道 Y 染色体的详细组织。为了研究黑腹果蝇的 Y 染色体组织，我们开发了一种组装策略，涉及异染色质长单分子读数的计算机富集，并使用这些读数创建异染色质序列的靶向从头组装。我们使用 Illumina 读数将重叠群分配给 Y 染色体，以识别男性特异性序列。我们的管道将黑腹果蝇参考基因组扩展了 11.9 Mb，缩小了 43.8% 的差距，并提高了整体连续性。添加 10.6 MB 的 Y 连锁序列使我们能够研究 Y 染色体上重复序列和基因的组织。我们检测到 Y 染色体的中心周区域与基因组其他区域的复制率很高。大多数这些重复基因以多个拷贝的形式存在。我们详细介绍了一种与性别相关的基因家族——星状晶体的进化史。虽然 Y 染色体不会发生交叉，但与全基因组估计值相比，我们观察到晶体星状基因家族 Su(Ste) 和 PCKR 成员内部和成员之间的基因转换率较高。我们的结果表明基因转换和基因复制在 Y 连锁基因的进化中发挥着重要作用。
Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore under-represented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family, crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.