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

Abstract

Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in range 910 - 940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader (SL) trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.

The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

“…The few xenacoelomorph genomes available to date are from the acoel Hofstenia miamia 16 – like other Acoelomorpha it shows accelerated sequence evolution relative to Xenoturbella 3 – and from two closely related species Praesagittifera naikaiensis 17 and Symsagittifera roscoffensis 18 . The analyses of gene content of Hofstenia showed similar numbers of genes and gene families to other bilaterians 16 , while an analysis of the neuropeptide content concluded that most bilaterian neuropeptides were present in Xenacoelomorpha 19 .…”

The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes

“…All the genome metrics, including length, contiguity, number of genes, and completeness, among others, were compared to the acoel genomes from P. naikaiensis ( Arimoto et al, 2019 )⁠ and S. roscoffensis ( Martinez et al, 2022 )⁠, which were also tested for contaminants using BlobTools2, following the same pipeline and with the same filtering criteria. The genomes of H. miamia and X. bocki ( Gehrke et al, 2019 ; Schiffer et al, 2023 ) were not considered because an annotation file with details of protein structure is not available for any of them.…”

“…Yet, this approach is recommended for genomes smaller than 500 Mb (PacBio’s library prep protocol), and it is unclear how well it performs beyond that limit, which is not a minor detail. Despite the general trend that miniaturised animals tend to have smaller genomes ( Liu et al, 2012 ; Gross et al, 2019 ; Xu et al, 2021 )⁠, there are several animals, such as Xenacoelomorpha, whose genome size is comparable to that of larger animals ( Arimoto et al, 2019 ; Gehrke et al, 2019 ; Martinez et al, 2022 ).…”

“…Several xenacoelomorph species have drawn interest as model systems to study the evolution of body regeneration, the nervous system, and endosymbiosis ( Martín-Durán et al, 2018 ; Andrikou et al, 2019 ; Gehrke et al, 2019 )⁠, resulting in the generation of genomes from Xenoturbella [ Xenoturbella bocki ; ( Schiffer et al, 2023 )] and Acoela [ Hofstenia miamia and the closely related acoel species Praesagittifera naikaiensis and Symsagittifera roscoffensis ; ( Arimoto et al, 2019 ; Gehrke et al, 2019 ; Martinez et al, 2022 )]. Thus, to fully capture the diversity of Xenacoelomorpha it is necessary to generate new genomes from Nemertodermatida, the sister group of Acoela from which it diverged more than 400 MYBP ( Dos Reis et al, 2015 ).…”

Acoelomorph flatworm monophyly is a severe long branch-attraction artefact obscuring a clade of Acoela and Xenoturbellida

“…Given the importance to understanding bilaterian evolution, resolving their placement among other animals has understandably been the main goal of phylogenomic analyses including Xenacoelomorpha 18,25,26,28 . Combined with such studies generally and expectedly recovering monophyletic Acoela, Nemertodermatida, Acoelomorpha, and Xenoturbella 3,18,26 , and the paucity of genome data for the lineage (although this is beginning to change 9,26,[43][44][45] ), this has resulted in little phylogenomic focus on internal xenacoelomorph relationships. Here, using both empirical and simulation approaches intended to detect and overcome phylogenomic error, I reassess the relationships between Xenoturbella and the fast evolving acoelomorph flatworms.…”