A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome

Abstract

<i>Apis cerana</i> is one of the main honeybee species in artificial farming, which is widely distributed in Asian countries. The genome of <i>A. cerana</i> has been sequenced by several different research groups using second generation sequencing technologies. However, it is still necessary to obtain more complete and accurate genome sequences. Here we present a chromosome-scale assembly of the <i>A. cerana</i> genome using single-molecule real-time (SMRT) Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated assembly is 215.67 Mb in size with a contig N50 of 4.49 Mb, representing an 212-fold improvement over the previous Illumina-based version. Hi-C scaffolding resulted in 16 pseudochromosomes occupying 97.85% of the assembled genome sequences. A total of 10,741 protein-coding genes were predicted and 9,627 genes were annotated. Besides, 314 new genes were identified compared to the previous version. The improved high-quality <i>A. cerana</i> reference genome will provide precise sequence information for biological research of <i>A. cerana</i>.