Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while most annelids have maintained the conserved bilaterian genome structure, a group containing leeches and earthworms possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show leeches and earthworms to have the most highly rearranged genomes of any currently sampled bilaterian. We further show that bilaterian genomes can be classified into..., This study aimed to characterize interchromosomal rearrangements within the phylum Annelida. All available chromosome-level assemblies of annelid species (n = 24) were obtained from the National Center for Biotechnology Information (NCBI) using NCBI Datasets on February 1st, 2024. Of the 24 genomes, 16 were produced by the Darwin Tree of Life (DToL) sequencing project (The Darwin Tree of Life Project Consortium et al. 2022). The genome assemblies from the DToL project have been made publicly available to the community for further analysis. Those with an accompanying publication are Acholoe squamosa (Adkins et al. 2023), Alitta virens (Fletcher et al. 2023), Lepidonotus clava (Darbyshire et al. 2022), Piscicola geometra (Doe et al. 2023), and Sthenelais limicola (Darbyshire et al. 2023). Genomes from other sources with accompanying publications are: Branchipolynoe longqiensis (He et al. 2023), Hirudinaria manillensis (Liu et al. 2023), Metaphire vulgaris (Jin et al. 2020), Owenia fusifor..., , # Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

[https://doi.org/10.5061/dryad.brv15dvhv](https://doi.org/10.5061/dryad.brv15dvhv)

## Description of the data and file structure

Gene models for 23 annelid species are available in GTF (.gtf), coding sequence (.fasta), and amino acid (.faa) formats. These 23 species are listed below:

* *Acholoe squamosa*
* *Alentia gelatinosa*
* *Alitta virens*
* *Amphiduros pacificus*
* *Aporrectodea icterica*
* *Bimastos eiseni*
* *Brachipolynoe longqiensis*
* *Branchellion lobata*
* *Harmothoe impar*
* *Hirudinaria manillensis*
* *Lamellibrachia columna*
* *Lepidonotus clava*
* *Lumbricus rubellus*
* *Lumbricus terrestris*
* *Metaphire vulgaris*
* *Paraescarpia echinospica*
* *Piscicola geometra*
* *Protula* sp. h YS2021
* *Sipunculus nudus*
* *Sthenelais limicola*
* *Streblospio benedicti*
* *Terebella lapidaria*
* *Urechis unicinctus*