Manual superscaffolding of honey bee (Apis mellifera) chromosomes 12–16: implications for the draft genome assembly version 4, gene annotation, and chromosome structure

The euchromatic arms of the five smallest telocentric chromosomes in the honey bee genome draft Assembly v4 were manually connected into superscaffolds. This effort reduced chromosomes 12–16 from 30, 21, 25, 42, and 21 mapped scaffolds to five, four, five, six, and five superscaffolds, respectively, and incorporated 178 unmapped contigs and scaffolds totalling 2.6 Mb, a 6.4% increase in length. The superscaffolds extend from the genetically mapped location of the centromere to their identified distal telomeres on the long arms. Only two major misassemblies of 146 kb and 65 kb sections were identified in this 23% of the mapped assembly. Nine duplicate gene models on chromosomes 15 and 16 were made redundant, while another 15 gene models were improved, most spectacularly the MAD (MAX dimerization protein) gene which extends across 11 scaffolds for at least 400 kb.