The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture that was originally developed for investigating the long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi-C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi-C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome-scale genome assemblies using single-copy reference orthologues.

中文翻译：

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Hi-C 支架的技术考虑和染色体规模基因组组装的评估


基于染色体规模基因组序列的大量信息的引入推动了生态研究的最新发展，即使对于无法获得遗传连锁的物种也是如此。这主要是通过 Hi-C 的应用实现的，Hi-C 是一种全基因组染色体构象捕获方法，最初是为研究染色质的长程相互作用而开发的。使用 Hi-C 数据执行基因组支架对资源的要求很高，并且需要采用复杂的实验室步骤来进行样品制备。它首先构建初级基因组序列组装作为输入，然后使用 Hi-C 数据计算基因组支架，需要仔细验证。本文介绍了获得最佳 Hi-C 脚手架结果的技术考虑因素，并提供了其应用于爬行动物物种马达加斯加地面壁虎 ( Paroedura picta ) 的测试案例。在经常用于评估支架结果的指标中，我们研究了使用单拷贝参考直向同源物对染色体规模基因组组装进行完整性评估的有效性。