Where are we now? Part 7 – Refinement of genome assemblies 25.05.22

We are finalizing the genome assembly of the Ponza grayling Hipparchia sbordonii, which is currently undergoing a manual refinement step. A comparative assessed of different de novo assembly strategies identified Canu as the best-performing algorithm: following different polishing and scaffolding steps, the genome assembly included 99 scaffolds (N50 = 10019938, L50 = 28 and BUSCO completeness = 98.6%). This was definitely a good achievement, even though the quality of the assembly still did not reach a chromosome level!

Thus, we decided to exploit synteny data to improve the contiguity of the Ponza grayling assembly, using the available high-quality genomes of Pararge aegeria (which belongs to the same subfamily Satyrinae) as a reference to build a map of orthologous genes. The Canu assembly was improved by using the scaffolds generated with other assembly approaches for gap-filling, whenever possible. This manual curation step brought the assembly to a near-chromosome level, significantly improving all relevant metrics (N50 = 14947868, L50 = 11 and a BUSCO = 98.7%). The recent publication of the genome of the congeneric species H. semele will allow us to further validate the reliability of this approach.

Comparison between the chromosomes of Pararge aegeria (left) and the scaffolds obtained in Hipparchia sbordonii after manual curation. Colored lines connect orthologous genes in the two species.

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