False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.
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DOI：
10.1186/s13059-022-02765-0
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发表时间：
2022-09-27
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
已经发现许多短读段基因组组装是不完整的并且包含错误组装。脊椎动物基因组计划一直在生产新的参考基因组组装，重点是尽可能完整和无错误，这需要利用长读段，长距离脚手架数据，新的组装算法和人工策展。对最近的参考文献相对于先前的组件进行更全面的评估，可以提供改进类型和幅度的详细概述。在这里，我们评估新的脊椎动物基因组参考相对于以前的组件相同的物种，在两种情况下，相同的个人，包括哺乳动物（鸭嘴兽），两种鸟类（斑胸草雀，安娜的蜂鸟），和鱼（攀鲈）。我们发现，高达11%的基因组序列是完全丢失在以前的组装。在脊椎动物基因组计划斑马雀大会，我们确定了八个新的GC和重复丰富的微染色体具有高基因密度。缺失序列的影响偏向于富含GC的5′-近端启动子和蛋白质编码基因的5′外显子区域以及长的非编码RNA。26%到60%的基因包含结构或序列错误，这可能导致在使用以前的基因组组装时对其功能的误解。我们的研究结果揭示了新的监管景观和蛋白质编码序列，这些序列在以前的组装中被大大低估，现在存在于脊椎动物基因组计划参考基因组中。在线版本包含补充材料，可通过10.1186/s13059-022-02765-0获得。
Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements. Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna’s hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5′-proximal promoters and 5′ exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies. Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes. The online version contains supplementary material available at 10.1186/s13059-022-02765-0.
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影响因子：
5.8
作者：
Hickey, Glenn;Paten, Benedict;Haussler, David
通讯作者：
Haussler, David
影响因子：
46.9
作者：
Cheng, Haoyu;Jarvis, Erich D.;Fedrigo, Olivier;Koepfli, Klaus-Peter;Urban, Lara;Gemmell, Neil J.;Li, Heng
通讯作者：
Li, Heng
影响因子：
14.9
作者：
Benson, Dennis A.;Karsch-Mizrachi, Ilene;Sayers, Eric W.
通讯作者：
Sayers, Eric W.
影响因子：
4.6
作者：
Dutta, Sunit;Dawid, Igor B.
通讯作者：
Dawid, Igor B.
DOI：
10.1261/rna.047324.114
发表时间：
2015-03
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Haerty W;Ponting CP
通讯作者：
Ponting CP