A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility
A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility
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蝴蝶泛基因组揭示了染色质可及性进化背后的大量结构变异
DOI：
10.1101/2022.04.14.488334
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
McMillan, W. Owen
中科院分区：
文献类型：
--
作者：
Ruggieri, Angelo A.;Livraghi, Luca;Lewis, James J.;Cicconardi, Francesco;Hebberecht, Laura;Montgomery, Stephen H.;Ghezzi, Alfredo;Rodriguez-Martinez, José Arcadio;Jiggins, Chris D.;McMillan, W. Owen
尽管插入和缺失是基因组中发现的最常见的结构变异（SV），但人们对这些SV在种群内和密切相关物种之间的差异有多大以及它们在进化中的重要性知之甚少。为了解决这些问题，我们使用三种密切相关的Heliconius蝴蝶物种的基因组组装来表征indel SV的进化。在相对较短的进化时间尺度调查，高达18.0%的基因组是由indels之间的两个单倍型的indels的一个individualHeliconius charithoniabutterus和高达62.7%的包括谱系特异性SV之间的基因组的最远的物种（11 Mya）。谱系特异性序列的主要特征是在整个基因组中随机插入的转座因子（TE），它们的总体分布也受到连锁选择的影响，如单核苷酸取代。使用染色质可及性概况（即，ATAC-seq）来鉴定具有潜在顺式调节功能的序列，我们发现在31，066个物种间染色质可及性的鉴定差异中，30.4%在谱系特异性SV内，9.4%被表征为TE插入。这些TE插入定位更接近基因转录起始位点比预期的随机和丰富的网站与几个转录因子结合位点具有显着的相似性，已知的功能在神经元发育inDrosophila。我们还确定了24 TE插入与头部特异性染色质可及性。我们的研究结果表明，以前被忽视的比较基因组研究的结构基因组进化的高速率，并建议一个高潜力的结构变异作为适应性进化的原材料。
Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely relatedHeliconiusbutterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individualHeliconius charithoniabutterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potentialcis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription factor binding sites with known function in neuron development inDrosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.8
作者：
Simao, Felipe A.;Waterhouse, Robert M.;Zdobnov, Evgeny M.
通讯作者：
Zdobnov, Evgeny M.
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DOI：
--
发表时间：
2020
影响因子：
11.1
作者：
S. Montgomery;Matteo Rossi;W. McMillan;R. Merrill
通讯作者：
R. Merrill
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影响因子：
2.1
作者：
Stephen H. Montgomery;Stephen H. Montgomery;R. Merrill
通讯作者：
R. Merrill
影响因子：
9.8
作者：
Moest，Markus;Van Belleghem，Steven M.;Jiggins，Chris D.
通讯作者：
Jiggins，Chris D.