Effect of sequence depth and length in long-read assembly of the maize inbred NC358

第一作者：Shujun Ou

第一单位：美国爱荷华州立大学

通讯作者：Doreen Ware

 Abstract 

背景回顾：Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. 

 摘  要 

长读长数据和scaffolding技术的提升对于复杂基因组组装质量的提升具有非常大的促进作用。然而，测序深度以及读长长度的评估对于合理配置资源仍然十分重要。为了这个目标，作者对于玉米自交系NC358基因组进行了三代测序，并利用20×到75×不同深度、11kb到21kb不同读长的PacBio测序数据产生了8个组装版本。作者发现用小于30×测序深度、subread N50长度小于11 kb的PacBio数据组装获得的基因组过于片段化。而当测序深度低到20×的时候，甚至低拷贝基因区的组装也十分不理想。进一步的分析发现基因组上基因、转座子元件以及端粒、异染色质纽和着丝粒等等高重复基因组区域序列的“完美”组装需要的测序深度和读长长度条件不一样。另外，作者还发现高质量的光学图谱可以显著提高基因组组装的连续性。在长读长测序技术日渐成熟的今天，本文的研究为进一步资源合理配置提供了一个参考。

 Discussion 

Recent innovations in long-read and scaffolding technology have made highly contiguous assembly possible across a wide range of species. We have documented how both the completeness and contiguity of assemblies improve with increasing depth and read length. The biological aims of an investigation must be considered when determining the level of investment in depth of sequence. With long-read sequencing, the low-copy gene space (including tandem gene arrays) can be well assembled with as low as 30× genomic coverage across a range of read lengths. Complete characterization of TEs in complex genomes such as maize will require a greater depth of sequence (~40×) and should employ library preparation protocols that maximize read-length N50. Finally, complete assembly of highly repetitive genomic features such as heterochromatic knobs, telomeres, and centromeres will require substantially more data. In fact, complete assembly of these latter highly repetitive sequences will likely require innovations beyond current sequencing technology.

doi: 10.1038/s41467-020-16037-7

Journal: Nature Communications

Published date: May 08, 2020