Durum wheat is a commercially valuable cereal crop with a large 10.45 gigabase allotetraploid genome. The PacBio Revio’s highly accurate long reads allow to sequence genomes of this scale at a much more affordable cost. At present, there have been no comprehensive studies investigating the effects of sequencing coverage on de novo genome assemblies for large plant genomes. To evaluate the impact of sequencing coverage on assembly completeness, we developed 14 genome assemblies with PacBio’s HiFi reads across a gradient of coverage ranging from 3.05× to 34.05×. We compiled and evaluated assembly statistics, gene features, and benchmarks of universal single-copy orthologs across the genome assemblies. The results highlight key differences in assembly features that result from coverage variation. These analyses will help researchers make informed decisions in determining a target coverage range for large germplasm resequencing projects. We demonstrate that aside from contig numbers and N and L metrics, durum wheat assemblies prepared at v8–10× coverage display genomic features nearly identical to the highly contiguous assemblies obtained from 15–34× coverage. These observations mark the 8–10× coverage as an optimal range for applications where a reference-grade reference assembly is available, thus enabling the resequencing of broad germplasm collections and maximizing sequencing outcomes.

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Genome Assembly Completeness of the Durum Wheat Genome as a Function of PacBio HiFi Sequencing Coverage

  • Md Nafis Ul Alam,
  • Marco Maccaferri,
  • Roberto Tuberosa,
  • Rod Wing,
  • Dario Copetti

摘要

Durum wheat is a commercially valuable cereal crop with a large 10.45 gigabase allotetraploid genome. The PacBio Revio’s highly accurate long reads allow to sequence genomes of this scale at a much more affordable cost. At present, there have been no comprehensive studies investigating the effects of sequencing coverage on de novo genome assemblies for large plant genomes. To evaluate the impact of sequencing coverage on assembly completeness, we developed 14 genome assemblies with PacBio’s HiFi reads across a gradient of coverage ranging from 3.05× to 34.05×. We compiled and evaluated assembly statistics, gene features, and benchmarks of universal single-copy orthologs across the genome assemblies. The results highlight key differences in assembly features that result from coverage variation. These analyses will help researchers make informed decisions in determining a target coverage range for large germplasm resequencing projects. We demonstrate that aside from contig numbers and N and L metrics, durum wheat assemblies prepared at v8–10× coverage display genomic features nearly identical to the highly contiguous assemblies obtained from 15–34× coverage. These observations mark the 8–10× coverage as an optimal range for applications where a reference-grade reference assembly is available, thus enabling the resequencing of broad germplasm collections and maximizing sequencing outcomes.