ArticleFunctional & integrative genomics2026
Dual-reference projection defines a callable core and reference-sensitive shell in a Qiantang River Megalobrama draft assembly.
Article in Functional & integrative genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Short-read genome projects in non-model fishes are often interpreted in chromosome-scale coordinates before assemblies can support chromosome-scale claims. We examined this problem in the Qiantang River Megalobrama sample SJF by projecting one polished Illumina-derived substrate onto two chromosome-level Megalobrama amblycephala references, defined as reference A (National Center for Biotechnology Information) and reference B (Genome Warehouse). Using 670,751,604 filtered reads (100.14 Gb), we first characterized genome architecture and compared candidate short-read substrates before projection. The analysis separated substrate quality from projected-coordinate interpretation. K-mer spectra estimated a 906.7-909.0 Mb haploid genome, 1.18-1.20% heterozygosity, and 34.7% repeat content, consistent with fragmentation in an Illumina-only draft. The raw MaSuRCA draft spanned 1.072 Gb across 519,765 scaffolds, whereas the Platanus donor draft was inflated (1.874 Gb). NextPolish refinement preserved draft-level Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness (34.1%) while improving consensus and read-backed support, so the NextPolish-refined MaSuRCA derivative was carried forward. Projection recovered 95.5-97.9% complete BUSCOs as projected gene-space representation. Reference choice affected anchored span much more than the correction step: reference A anchored 919.17-919.24 Mb, whereas reference B anchored 878.98-879.06 Mb. Yet 50-kb concordance remained high (92.47-96.95% one-to-one), callable fractions were nearly identical (77.24-77.35%), and callable core sequence reached 724.85-727.35 Mb. Gene-interval partitioning further placed most transferred gene-bearing sequence in the callable core. The benchmark therefore defines a large callable core and a smaller reference-sensitive shell that delimit where local sequence and reference-addressed interpretation are best supported in a fragmented short-read draft.
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