Evaluating long-read assemblers to assemble several aphididae genomes.

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.