A Novel Hybrid Approach for Drafting Chromosome-Level Genome Assemblies Applied to Avian Genomes

The next-generation sequencing technologies made sequencing an animal genome a routine procedure, leading to a substantial increase in the number of available genome assemblies. However, most assemblies are highly fragmented limiting their use in genome evolution, genotype-to-phenotype association and disease mapping studies. To start resolving this issue we here present a novel scaffold-to-chromosome anchoring approach combining: a) the reference-assisted chromosome assembly (RACA) and b) wet-lab techniques (PCR and zoo-FISH) to position scaffolds from assemblies with N50 >1-2Mb along chromosomes. Briefly, for a de novo sequenced genome RACA utilises the raw reads and comparative data to order scaffolds into ‘predicted chromosome fragments’ (PCFs). The PCF accuracy is verified using PCR across the regions of broken synteny between the de novo assembled and closely related genomes and false-joints are eliminated. The PCFs are then ordered along chromosomes using in situ hybridization (zoo-FISH) of a sparse set of BAC clones specially selected from evolutionary conserved intervals of multiple genomes. This ensures that the same set of clones is suitable for mapping related species. We currently apply our approach to 18 avian genomes. The verified PCF sets generated represent a reduction in the number of scaffolds by up to ~90% leading to a 3-17x increase in the assembly N50. Moreover, we produced drafts of chromosome assemblies for peregrine falcon and rock pigeon genomes. Our approach will facilitate a more detailed study of avian karyotype evolution and roles of chromosome rearrangements in adaptation and phenotypic diversity in birds and facilitate mapping of avian disease phenotypes.