Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure

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 fi..., Chromosome-scale assemblies of Bugulina stolonifera (GenBank accession no. GCA_935421135), Cryptosula pallasiana (GCA_945261195), Membranipora membranacea (GCA_914767715), and Watersipora subatra (GCA_963576615) were sequenced as part of the Darwin Tree of Life project and retrieved from the NCBI Datasets. A chromosome-scale assembly of Cristatella mucedo 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., , # **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.

在漫长的进化历程中，同源基因（orthologous gene）通常会共同保留在同一条染色体上。这种广泛的物理基因连锁现象被称为宏观共线性（macrosynteny），在脊索动物门（Chordata）、棘皮动物门（Echinodermata）、软体动物门（Mollusca）和纽形动物门（Nemertea）等分化程度极高的两侧对称动物门类之间均能观察到，这一现象大概率反映了基因组组织结构对基因调控景观的重要意义。

本研究聚焦于研究程度较低的群居无脊椎动物门类——苔藓动物门（Bryozoa），报道了该类群独特的基因组进化模式。本研究借助包含系统发育重建（phylogenetic reconstruction）与同源基因定位（orthologous gene mapping）在内的比较基因组学（comparative genomics）手段，重构了5种苔藓动物的染色体进化历程。我们推断出苔藓动物祖先的基因组组织结构，并鉴定出多轮古老的染色体融合事件伴随基因混合，最终导致两侧对称动物连锁群近乎完全丢失。随后发生第二轮基因组重排浪潮，包含染色体分裂（chromosome fission）事件，该事件在两个苔藓动物纲中独立发生，进一步打乱了苔藓动物的基因组结构。我们还发现至少有……

匍匐管孔虫（Bugulina stolonifera，GenBank登录号：GCA_935421135）、隐囊虫（Cryptosula pallasiana，GCA_945261195）、膜孔虫（Membranipora membranacea，GCA_914767715）和沃氏苔虫（Watersipora subatra，GCA_963576615）的染色体级基因组组装（chromosome-scale assembly）均由达尔文生命之树计划（Darwin Tree of Life project）测序完成，并从NCBI数据集（NCBI Datasets）中获取。冠虫（Cristatella mucedo）的染色体级基因组组装则从NCBI基因表达汇编（NCBI Gene Expression Omnibus，登录号GSE169088）中获取。

本研究使用的所有苔藓动物基因组组装结果均未公开提供可用的基因模型，因此我们在本实验室内部完成了基因预测。首先使用RepeatModeler（v2.0.4）注释重复序列元件，并以敏感模式通过RepeatMasker（v4.1.5）进行序列屏蔽。随后借助BRAKER3分析流程（v3.0.3）完成基因预测与注释，该流程整合了以BAM格式（BAM format）存储的比对后RNA测序（RNA-seq）读段作为预测辅助信息。

# **苔藓动物基因组揭示广泛的染色体重排与两侧对称动物基因组结构的演化**

https://doi.org/10.5061/dryad.76hdr7t3f

## 数据与文件结构说明

本数据集包含全部5种苔藓动物的基因模型，分别为匍匐管孔虫（Bugulina stolonifera，缩写Bst）、冠虫（Cristatella mucedo，缩写Cmu）、隐囊虫（Cryptosula pallasiana，缩写Cpa）、膜孔虫（Membranipora membranacea，缩写Mme）以及沃氏苔虫（Watersipora subatra，缩写Wsu），数据格式包括GTF（.gtf）、编码序列（.fa）与氨基酸序列（.faa）。