Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.

中文翻译：

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全基因组比对和比较注释。

快速改进的测序技术加上序列组装计算的发展使得参考质量的基因组组装变得经济。数百个脊椎动物基因组组装现已公开，并且正在提议在未来几年内对数千个其他物种进行测序的项目。对生命之树进行如此密集的采样应该会给进化带来前所未有的新认识，并能够详细确定导致我们周围丰富的生物多样性的事件。为了获得这些知识，必须通过基因组比对（在序列水平）和比较注释（在基因水平）来比较这些新基因组。然而，不同的对齐和标注方法有不同的特点；在开始比较基因组学分析之前，了解所选方法的性质以及固有的偏差和局限性非常重要。本次审查旨在作为该领域的技术性但高层次的概述，以提供这种理解。我们简要调查了基因组比对和比较注释领域的现状以及这些领域在新的大规模比较基因组学时代的潜在未来方向。