The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

Abstract

The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data, which can help to elucidate phylogenetic relationships and provide important comparative data, remain sparse for early branching bilaterians. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of ~110 Mbp in 18 chromosome like scaffolds, with repeat content, and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.

Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on photosymbiosis

“…The GC content of this genome amounts to 36.7% (Table 2), so S. roscoffensis can be considered as having an AT-rich genetic makeup. The composition fits well in the range observed for other xenacolomorphs (43% GC content in X. bocki (Schiffer et al 2022), or 39.1% GC content in P. naikaiensis (Arimoto et al 2019); all of them, also, enriched in A+T nucleotides.…”

“…In the assembled genomes of acoels, the content of repetitive sequences varies from a value of 53% in H. miamia to 61% in S. roscoffensis and the largest estimated value of 70% in P. naikaiensis . Moreover, in the related group of xenoturbellids, a recent sequencing project has revealed that the species X. bocki has a surprisingly low fraction of repeats, around 25% (Schiffer et al 2022). Interestingly, X. bocki also has a relatively compact genome of ~110 Mb (Schiffer et al 2022).…”

“…Moreover, in the related group of xenoturbellids, a recent sequencing project has revealed that the species X. bocki has a surprisingly low fraction of repeats, around 25% (Schiffer et al 2022). Interestingly, X. bocki also has a relatively compact genome of ~110 Mb (Schiffer et al 2022). In fact, the fraction of repeats is directly correlated with the estimated size of the genomes and in cases of S. roscoffensis and H. miamia it is in the same range, though P. naikaiensis is an example that clearly deviates from those values and ratios.…”

“…Mb (Schiffer et al 2022). In fact, the fraction of repeats is directly correlated with the estimated size of the genomes and in cases of S. roscoffensis and H. miamia it is in the same range, though P.…”

Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis

“…The GC content of S. roscoffensis genome is 36.7% ( Table 1 ), thus it is an AT-rich genome, similar to other xenacolomorphs [43% GC content in Xenoturbella bocki ( Schiffer et al 2022 ), 39.1% GC content in P. naikaiensis ( Arimoto et al 2019 )].…”