The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, and population genomics of naturally occurring species. Moreover, the extent to which a single reference genome represents the diversity within a species varies: pan‐genomes will become increasingly important ecological genomics resources, particularly in systems found to have considerable presence‐absence variation in their functional content. Here, we highlight advances in technology that have raised the bar for genome assembly and provide guidance on standards to achieve exceptional quality reference genomes. Key recommendations include the following: (a) Genome assemblies should include long‐read sequencing except in rare cases where it is effectively impossible to acquire adequately preserved samples needed for high molecular weight DNA standards. (b) At least one scaffolding approach should be included with genome assembly such as Hi‐C or optical mapping. (c) Genome assemblies should be carefully evaluated, this may involve utilising short read data for genome polishing, error correction, k‐mer analyses, and estimating the percent of reads that map back to an assembly. Finally, a genome assembly is most valuable if all data and methods are made publicly available and the utility of a genome for further studies is verified through examples. While these recommendations are based on current technology, we anticipate that future advances will push the field further and the molecular ecology community should continue to adopt new approaches that attain the highest quality genome assemblies.

中文翻译：

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基因组组装的变化面：实现高质量参考基因组的指南

由于测序技术、组装方法和质量控制的不断进步，基因组组装的质量近年来迅速提高。在分子生态学领域，这导致了高质量基因组组装的发展，这些组装将成为更广泛研究自然物种的生态、保护、进化和种群基因组学的重要长期资源。此外，单个参考基因组代表物种内多样性的程度各不相同：泛基因组将成为越来越重要的生态基因组学资源，特别是在发现其功能内容存在显着差异的系统中。这里，我们强调了提高基因组组装门槛的技术进步，并提供了标准指导，以实现卓越的质量参考基因组。主要建议包括以下内容：(a) 基因组组装应包括长读长测序，除非在极少数情况下实际上不可能获得高分子量 DNA 标准所需的充分保存的样本。(b) 基因组组装中至少应包含一种支架方法，例如 Hi-C 或光学作图。(c) 应仔细评估基因组组装，这可能涉及利用短读数据进行基因组完善、纠错、k-mer 分析，并估计映射回组装的读长百分比。最后，如果所有数据和方法都是公开可用的，并且基因组在进一步研究中的效用通过实例得到验证，那么基因组组装是最有价值的。虽然这些建议基于当前技术，但我们预计未来的进步将推动该领域进一步发展，分子生态学界应继续采用新方法来获得最高质量的基因组组装。