A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis

Abstract

Background 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 the 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, Praesagittifera naikaiensis . Findings 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 sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs 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. Conclusions Our present sequencing and assembly of the P. naikaiensis 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.

Structural and Functional Characterization of the FGF Signaling Pathway in Regeneration of the Polychaete Worm Alitta virens (Annelida, Errantia)

“…Additional bona fide FGF candidates were looked for in genome datasets for spiralians Capitella teleta and Lottia gigantea [ 44 ] and the basally divergent bilaterian Praesagittifera naikaiensis [ 43 ]. Two unique sequences with characteristic domain organization were identified in the acoel worm P. naikaiensis , one in the polychaete Capitella teleta , and two in the mollusk L. gigantea .…”

“…Sequences of FGF and FGFR were found in an unannotated transcriptome database for Alitta virens (local resource), Platynereis dumerilii databases ( ; accessed on 1 November 2018), genome assembly for Praesagittifera naikaiensis [ 43 ] ( accessed on 1 April 2021), Capitella teleta and Lottia gigantea [ 44 ] ( accessed on 1 April 2021) and in the publicly available molecular genetic databases GenBank and UniProt via TBLASTN search. The sequences were analyzed and aligned in the CLC Workbench.…”

Extensive loss of Wnt genes in Tardigrada

“…First, we note that, in addition to tardigrades, several other secondarily miniaturized animals exhibit extensive loss of Wnt genes (Fig. 10 , Caenorhabditis , Adineta , Schmidtea , Dimorphilus , Hofstenia ) [ 3 , 5 , 97 , 106 , 107 ]. The extensive loss of Wnt genes in some secondarily miniaturized animals may be due to the evolution of simpler cell fate specification mechanisms related to reduction in cell number and simplified morphology that often accompanies miniaturization.…”

Xenacoelomorpha flatworms are basal Deuterostome

“…Adult specimens of Heterochaerus australis been cultured and asexual reproduced in laboratory. DNA was isolated from adult specimens after starved two weeks totally shaded to avoid contamination by their food and symbiosis algae, extracted total DNA as described in A Arimoto et al [38]. Sequencing, assembling and annotation are carried out as described in Felix Guerrero et al [39].…”