Evaluating long-read assemblers to assemble several aphididae genomes

Aphids are a speciose family of the Hemiptera compromising >5500 species. They have adapted to feed off multiple plant species and occur on every continent on Earth. Although economically devastating, very few aphid genomes have been sequenced and assembled, and those that have suffer low contiguity due to repeat-rich and AT-rich genomes. With third-generation sequencing becoming more affordable and approaching quality levels to that of second-generation sequencing, the ability to produce more contiguous aphid genome assemblies is becoming a reality. With a growing list of long-read assemblers becoming available, the choice of which assembly tool to use becomes more complicated. In this study, six recently released long-read assemblers (Canu, Flye, Hifiasm, Mecat2, Raven, and Wtdbg2) were evaluated on several quality and contiguity metrics after assembling four populations (or biotypes) of the same species (Russian wheat aphid, Diuraphis noxia) and two unrelated aphid species that have publicly available long-read sequences. All assemblers did not fare equally well between the different read sets, but, overall, the Hifiasm and Canu assemblers performed the best. Merging of the best assemblies for each read set was also performed using quickmerge, where, in some cases, it resulted in superior assemblies and, in others, introduced more errors. Ab initio gene calling between assemblies of the same read set also showed surprisingly less similarity than expected. Overall, the quality control pipeline followed during the assembly resulted in chromosome-level assemblies with minimal structural or quality artefacts.