Planning of pipelines for next-generation sequencing (NGS) projects could be facilitated by using simple DNA sequence benchmarks, i.e., standard test sequences that could monitor or help to predict ease or difficulty of (a) short-read sequencing and (b) de novo assembly of the sequenced reads. We propose that familiar, gene-sized sequences, including but not limited to nuclear protein-coding genes, would provide feasible consensus benchmarks allowing simple visualization. We illustrate our proposal for fungi with candidates from ribosomal DNA (rDNA, used in phylogeny and identification/diagnostics), mitochondrial DNA (mtDNA), and combinatorially constructed conceptual (synthetic) DNA sequences. The exploratory analysis of such familiar candidate loci could be a step toward finding, testing and establishing familiar, biologically interpretable consensus benchmark sequences for fungal and other eukaryotic genomes.
