Australian Centre for Plant Functional Genomics, Institute for Molecular Biosciences and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039.
The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Until recently, the sequencing of even small model genomes required substantial funds and international collaboration. The development of 'second-generation' sequencing technology has increased the throughput and reduced the cost of sequence generation by several orders of magnitude. These new methods produce vast numbers of relatively short reads, usually at the expense of read accuracy. Since the first commercial second-generation sequencing system was produced by 454 Technologies and commercialised by Roche, several other companies including Illumina, Applied Biosystems, Helicos Biosciences and Pacific Biosciences have joined the competition. Because of the relatively high error rate and lack of assembly tools, short-read sequence technology has mainly been applied to the re-sequencing of genomes. However, some recent applications have focused on the de novo assembly of these data. De novo assembly remains the greatest challenge for DNA sequencing and there are specific problems for second generation sequencing which produces short reads with a high error rate. However, a number of different approaches for short-read assembly have been proposed and some have been implemented in working software. In this review, we compare the current approaches for second-generation genome sequencing, explore the future direction of this technology and the implications for plant genome research.
测序技术已成为现代生物学研究中最重要的工具之一。直到最近，即使是对小型模式基因组的测序也需要大量的资金和国际合作。“第二代”测序技术的发展使序列生成的通量和成本提高了几个数量级。这些新方法产生了大量相对较短的读取序列，通常是以牺牲读取准确性为代价的。自 454 技术公司生产出第一代商业性第二代测序系统并由罗氏公司商业化以来，Illumina、Applied Biosystems、Helicos Biosciences 和 Pacific Biosciences 等其他几家公司也加入了竞争。由于相对较高的错误率和缺乏组装工具，短读序列技术主要应用于基因组的重测序。然而，一些最近的应用集中在这些数据的从头组装上。从头组装仍然是 DNA 测序面临的最大挑战，对于产生高错误率的短读序列的第二代测序来说，还有一些特定的问题。然而，已经提出了许多用于短读序列组装的不同方法，其中一些已经在工作软件中得到了实现。在本综述中，我们比较了第二代基因组测序的当前方法，探讨了这项技术的未来发展方向及其对植物基因组研究的影响。
