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 orthologs, and report problems of the widely used program pipeline BUSCO.

Recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species whose genetic linkage was previously not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture which was originally developed for investigating long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding in elaborate laboratory steps for sequencing sample preparation, building primary genome sequence assembly as an input, and computation for genome scaffolding using Hi-C data, followed by careful validation. This article summarizes existing solutions for these steps and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among frequently exerted metrics for evaluating scaffolding results, we investigate the validity of completeness assessment using single-copy reference orthologs and report problems with the widely used program pipeline BUSCO.