High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.
High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.
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高质量基因组组装揭示了果蝇 virilis 亚群中重复 DNA 和结构重排的进化动力学。
DOI：
10.1093/gbe/evad238
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发表时间：
2024-01-05
影响因子：
3.3
通讯作者：
Clark, Andrew G.
中科院分区：
文献类型：
--
作者：
Flynn, Jullien M.;Ahmed-Braimah, Yasir H.;Long, Manyuan;Wing, Rod A.;Clark, Andrew G.
关键词：
跨越一系列非传统模式生物的高质量基因组组装可以加速发现基因组进化的新方面。除了是物种形成遗传学的一个有吸引力的模式外，果蝇群还具有几个区别于果蝇属中研究程度更高的物种的属性，例如异常丰富的重复元素和广泛的核型进化。在这里，我们使用长阅读测序的方法组装了三个男性群体物种的五个基因组，并描述了序列和结构差异以及重复的DNA进化。我们发现，我们连续的基因组组装可以轻松地表征染色体排列，并有助于分析倒位断点。我们还利用一小部分重新测序的菌株来探索该物种中的差异和多态的基因组模式，并表明已知的人口历史在很大程度上预测了全基因组分离多态的程度。我们进一步发现，美洲果蝇的neo-X染色体显示出类似X的核苷酸多样性水平。我们还发现，不寻常的重复元件是物种间基因组组成差异的主要原因。与果蝇相比，美洲锥虫Y染色体上的氦衍生串联重复序列的丰度增加了两倍，这是这两个姐妹物种之间重复含量差异的主要原因。具有转座元件和卫星DNA特征的重复序列在美洲假丝酵母和诺氏假丝酵母中都扩大了3倍，主要是常染色质。我们的结果代表着我们对这一新兴模式分支中基因组生物学的理解取得了重大进展。
High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here, we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution. We find that our contiguous genome assemblies allow characterization of chromosomal arrangements with ease and can facilitate analysis of inversion breakpoints. We also leverage a small panel of resequenced strains to explore the genomic pattern of divergence and polymorphism in this species and show that known demographic histories largely predicts the extent of genome-wide segregating polymorphism. We further find that a neo-X chromosome in Drosophila americana displays X-like levels of nucleotide diversity. We also found that unusual repetitive elements were responsible for much of the divergence in genome composition among species. Helitron-derived tandem repeats tripled in abundance on the Y chromosome in D. americana compared to Drosophila novamexicana, accounting for most of the difference in repeat content between these sister species. Repeats with characteristics of both transposable elements and satellite DNAs expanded by 3-fold, mostly in euchromatin, in both D. americana and D. novamexicana compared to D. virilis. Our results represent a major advance in our understanding of genome biology in this emerging model clade.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
3.3
作者：
Ahmed-Braimah, Yasir H.;Sweigart, Andrea L.
通讯作者：
Sweigart, Andrea L.
影响因子：
2.9
作者：
BLIGHT, WC;ROMANO, A
通讯作者：
ROMANO, A
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
影响因子：
3.3
作者：
Fonseca, Nuno A.;Morales-Hojas, Ramiro;Vieira, Jorge
通讯作者：
Vieira, Jorge