Department of Genome Sciences, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, Washington, USA.
Nat Methods. 2011 Jan;8(1):61-5. doi: 10.1038/nmeth.1527. Epub 2010 Nov 21.
High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.
高通量测序技术有望在不久的将来为数万基因组的测序提供便利，从而彻底改变遗传学和比较生物学领域。虽然在短短几个月内构建从头基因组组装是可行的，但人们对单纯应用短序列读段所导致的信息缺失关注甚少。我们将基于短寡核苷酸分析包（SOAP）生成的中国汉族个体和非洲约鲁巴个体的全基因组从头组装与实验验证的基因组特征进行了比较。我们发现，从头组装的基因组比参考基因组短 16.2%，并且有 420.2 Mb 的常见重复序列和 99.1%的已验证重复序列缺失。结果，超过 2377 个编码外显子完全缺失。我们得出的结论是，在进行比较基因组学分析和研究基因组进化时，必须结合高质量测序方法考虑高通量测序。
