A draft genome assembly of the acoel flatworm Praesagittifera naikaiensis

Acoels are primitive bilaterians with very simple soft-bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in formation of the basic bilaterian body-plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel,<i> Praesagittifera naikaiensis</i>.<br>To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired end and mate-pair libraries) and PacBio sequencing. RNA-seq and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ~17-kbp mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nucleargenome assembly was ~656-Mbp in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb, respectively. Although ~70% of the assembled sequences were likely comprised of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein coding genes, approximately 99% of which were substantiated by corresponding transcripts.
We could not find horizontally-transferred microalgal genes in the acoel genome. BUSCO analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.<br> Our present sequencing and assembly of the <i>P. naikaiensis</i> nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.