MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes

BACKGROUND: Obtaining chromosomally complete genome assemblies across the tree of life is an important goal of biodiversity genomics. However, some lineages remain recalcitrant to assembly. Birds present a substantial assembly challenge due to the presence of tiny microchromosomes that are often highly fragmented or even missing in draft genome assemblies. Bird genomes therefore require substantial expert manual curation effort via manipulation of genome-wide HI-C contact maps and many chromosome-level bird genome assemblies do not resolve the known karyotype. FINDINGS: Here, using a reference set of expert curated bird genomes, we have identified a set of conserved proteins for the smallest and hardest to assemble microchromosomes-the dot chromosomes-and developed MicroFinder, a pipeline that uses this protein set to find small dot microchromosome fragments in draft genome assemblies to act as anchors for manual curation. We demonstrate how MicroFinder can be used to improve the speed and accuracy of bird genome curation. Furthermore, we highlight the usefulness of MicroFinder by carrying out MicroFinder-enabled re-curation of 12 previously released chromosome-scale bird genome assemblies, increasing the sequence content of dot microchromosome models. CONCLUSIONS: We present MicroFinder, a pipeline to identify and order putative dot microchromosome scaffolds in draft genome assemblies. MicroFinder is an effective aid for bird genome assembly that dramatically speeds up manual assembly curation and improves the accuracy and sequence content of bird dot microchromosomes, even enabling improvement to genome assemblies that have already undergone expert curation.