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Evaluating long-read assemblers to assemble several aphididae genomes.

Nicolaas F V Burger1, Vittorio F Nicolis1, Anna-Maria Botha1

  • 1Van der Byl Street, Genetics Department, JC Smuts Building, Faculty of AgriScience, Stellenbosch University, Stellenbosch, South Africa.

Briefings in Bioinformatics
|March 13, 2025
PubMed
Summary

Evaluating long-read assemblers is crucial for improving aphid genome assemblies. Hifiasm and Canu generally performed best, enabling high-quality, chromosome-level genome reconstructions for Diuraphis noxia.

Keywords:
aphid genomesassembly and QC pipelinegenome quality assessmentlong-read assemblymultiple assembly comparison

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Area of Science:

  • Genomics
  • Bioinformatics
  • Entomology

Background:

  • Aphids (Hemiptera: Aphididae) comprise over 5500 species, impacting agriculture globally.
  • Few aphid genomes are assembled due to repeat-rich, AT-rich genomes, hindering research.
  • Advancements in third-generation sequencing offer potential for more contiguous aphid genome assemblies.

Purpose of the Study:

  • To evaluate the performance of six contemporary long-read assemblers for aphid genome sequencing.
  • To compare assembly quality and contiguity across different aphid species and populations.
  • To identify optimal tools for generating high-quality, chromosome-level aphid genome assemblies.

Main Methods:

  • Assembly of four Diuraphis noxia populations and two other aphid species using six long-read assemblers (Canu, Flye, Hifiasm, Mecat2, Raven, Wtdbg2).
  • Evaluation of assemblers based on quality and contiguity metrics.
  • Application of quickmerge for merging assemblies and assessment of gene calling similarity.

Main Results:

  • Assembler performance varied across different read sets.
  • Hifiasm and Canu demonstrated superior performance overall.
  • Assembly merging with quickmerge yielded mixed results, sometimes improving and sometimes degrading assembly quality.
  • Ab initio gene calling showed lower-than-expected similarity between assemblies of the same read set.

Conclusions:

  • Hifiasm and Canu are recommended for generating contiguous aphid genome assemblies.
  • Careful quality control is essential for achieving chromosome-level assemblies with minimal artefacts.
  • Further investigation into assembly merging strategies and gene calling consistency is warranted.