DOI: 10.5061/dryad.76hdr7t3f
title: Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure

description: Orthologous genes are commonly found together on the same chromosome over
 vast evolutionary distances. This extensive physical gene linkage, known
 as macrosynteny, can be seen between bilaterian phyla as divergent as
 Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the
 importance of genome organization to gene regulatory landscapes. Here, we
 report a unique pattern of genome evolution in Bryozoa, an understudied
 phylum of colonial invertebrates. Using comparative genomics, including
 phylogenetic reconstruction and orthologous gene mapping, we reconstruct
 the chromosomal evolutionary history of five bryozoans. We infer the
 ancestral bryozoan genome organization and identify multiple ancient
 chromosome fusions followed by gene mixing, leading to the near-complete
 loss of bilaterian linkage groups. A second wave of rearrangements,
 including chromosome fission, occurred independently in two bryozoan
 classes, further shuffling bryozoan genomes. We also discover at least
 five derived chromosomal fusion events shared between bryozoans and
 brachiopods, supporting the traditional yet highly debated Lophophorata
 hypothesis. Finally, we show that chromosome fusion and fission processes
 led to the separation of bryozoan Hox clusters. Our findings demonstrate
 that the canonical bilaterian genome structure has been lost across an
 entire phylum, reveal that linkage group fission can occur very frequently
 in specific lineages, and provide a powerful source of phylogenetic
 information.
description: Chromosome-scale assemblies of
 <em>Bugulina</em><em> stolonifera</em> (GenBank
 accession no. GCA_935421135),
 <em>Cryptosula</em><em> pallasiana</em>
 (GCA_945261195),
 <em>Membranipora</em><em> membranacea</em>
 (GCA_914767715), and
 <em>Watersipora</em><em> subatra</em>
 (GCA_963576615) were sequenced as part of the Darwin Tree of Life project
 and retrieved from the NCBI Datasets. A chromosome-scale assembly of
 <em>Cristatella</em><em> mucedo</em> was obtained
 from the NCBI Gene Expression Omnibus (GSE169088). None of the bryozoan
 assemblies used have publicly available gene models, so gene prediction
 was performed in-house. Repetitive elements were first annotated with
 RepeatModeler (v2.0.4) and masked using RepeatMasker (v4.1.5) in sensitive
 mode. Gene prediction and annotation were performed using the BRAKER3
 pipeline (v3.0.3), incorporating hints from RNA sequencing (RNA-seq) data
 as aligned reads in bam format.
description: # **Bryozoan genomes reveal extensive chromosome rearrangement and the
 evolution of bilaterian genome structure**
 [https://doi.org/10.5061/dryad.76hdr7t3f](https://doi.org/10.5061/dryad.76hdr7t3f) ## Description of the data and file structure This dataset contains gene models for all five bryozoan species, including *Bugulina stolonifera* (Bst), *Cristatella mucedo* (Cmu), *Cryptosula pallasiana* (Cpa), *Membranipora membranacea* (Mme), and *Watersipora subatra* (Wsu) in GTF (.gtf), coding sequence (.fa), and amino acid (.faa) format.