AbstractThe planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S.

摘要正在研究涡虫Schmidtea mediterranea作为再生的模式物种，但涡虫基因组的组装仍然具有挑战性。在这里，我们报告了S.mediterranea有性S2菌株的高质量单倍型阶段性染色体规模基因组组装及其三个近亲S的高质量染色体规模组装。

polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations.

polychroa，S。nova和S。lugubris。使用杂交基因注释和优化的ATAC-seq和ChIP-seq协议进行调控元件注释，我们为涡虫研究界提供了有价值的基因组资源，并为涡虫基因组进化提供了第一个比较视角。我们的分析揭示了蛋白质编码序列和调控区的显着差异，但在启动子和增强子注释中具有相当大的保守性。

We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints..

我们还发现Schmidtea属中频繁的反转录转座子相关染色体倒位和染色体间易位，并且在Schmidtea和其他两个扁形虫组中，祖先后生动物的同源性明显独立且几乎完全丧失。总的来说，我们的结果表明，platyhelminth基因组可以在没有同线性约束的情况下进化。。

IntroductionEvolution acts on genomic changes to bring about the diversity of life. For example, single nucleotide changes in coding gene sequences duplicate the goldfish tail fin1 or cause nose loss in humans2; changes in gene regulatory regions are associated with profound evolutionary body plan changes3,4, e.g., limb loss in snakes5, and gene loss is emerging as an important mechanism in trait evolution6,7.

。例如，编码基因序列中的单核苷酸变化会复制金鱼尾鳍1或导致人类鼻子脱落2；基因调控区的变化与深刻的进化身体计划变化有关3,4，例如蛇的肢体丢失5，基因丢失正在成为性状进化的重要机制6,7。

On the other hand, the rapidly increasing number of sequenced genomes indicates that genome structure may also be evolutionarily constrained.Synteny, the association of genes on a chromosome or linkage group, is deeply conserved among animals, with the Metazoan Ancestral Linkage Groups (MALG) being conserved in numerous animal phyla, including Sponges, Cnidarians, and Bilateria8,9,10.

另一方面，测序基因组数量的迅速增加表明基因组结构也可能受到进化限制。同线性是染色体或连锁群上基因的关联，在动物中是高度保守的，后生动物祖先连锁群（MALG）在许多动物门中都是保守的，包括海绵，刺胞动物和双侧8,9,10。

Other groups, including Nematodes and Drosophilids, have lost this ancestral synteny, but have replaced it with group-specific linkage groups11,12. The finding that the arrangement of genes in the genome at the mega-base scale is important for gene regulation13 provides a rationale for the evolutionary conservation of synteny.

其他群体，包括线虫和果蝇，已经失去了这种祖先的同线性，但已经用群体特异性连锁群11,12取代了它。基因组中基因在兆碱基规模上的排列对于基因调控很重要的发现13为同线性的进化保守性提供了理论基础。

Indeed, molecular studies have shown that gene regulation is influenced by hierarchical levels of chromatin organization14 and that the modulation of chromatin organization can lead to genetic disease15,16, cancer17,18, or even the origin of evolutionary novelty19,20,21. However, not all taxa exhibit consistent features of genomic organization or their significance remains unclear22.

事实上，分子研究表明，基因调控受染色质组织层次水平的影响14，染色质组织的调节可导致遗传疾病15,16，癌症17,18，甚至是进化新颖性的起源19,20,21。然而，并非所有分类群都表现出基因组组织的一致特征，或者它们的意义尚不清楚22。

This raises the possibility that certain taxonomic groups may display specific patterns of genome evolution and that the analysis of under-sampled clades may reveal novel patterns.Planarians are an example of a large and poorly sequenced group of animals. As an order (Tricladida) w.

这提高了某些分类群可能显示基因组进化的特定模式的可能性，并且对采样不足的进化枝的分析可能揭示新的模式。涡虫是大型且测序不良的动物群的一个例子。作为订单（Tricladida）w。

Schmidtea mediterranea reference genome improvementsThe current S. mediterranea reference genome (dd_Smes_g426) is a haploid consensus assembly containing 481 contigs and its recent scaffolding (referred to here as schMedS2) has revealed substantial haplotypic differences, especially on Chromosome 127.

Schmidtea mediterranea参考基因组改进目前的S.mediterranea参考基因组（dd\U Smes\U g426）是包含481个重叠群的单倍体共有组装体，其最近的支架（此处称为schMedS2）显示出显着的单倍型差异，特别是在127号染色体上。

To generate a haplotype-phased assembly and to close the remaining sequencing gaps, we re-sequenced the S. mediterranea genome using Pacific Biosciences’ HiFi reads and used Hi-C for scaffolding. The new assembly, designated S3, consists of two pseudo-haplotypes: S3h1 and S3h2, and a merged version of the two, referred to as S3BH for “S3 both haplotypes”.

为了产生单倍型阶段组装并缩小剩余的测序缺口，我们使用Pacific Biosciences的HiFi读数对地中海链球菌基因组进行了重新测序，并使用Hi-C进行了支架。命名为S3的新组件由两个伪单倍型组成：S3h1和S3h2，以及两者的合并版本，称为S3BH，表示“S3都是单倍型”。

The S3h1 (662 contigs) and S3h2 (432 contigs) assemblies are slightly larger than the previous dd_Smes_g4 assembly (Table 1, Supporting Information: Section 1.1). The N50 values of 270 Mb and 269 Mb indicate high contiguity with 95% and 96% of the total assembly contained in the four largest scaffolds that match the known karyology in size and number (1n = 4, Table 1).

S3h1（662个重叠群）和S3h2（432个重叠群）组件略大于之前的dd\U Smes\U g4组件（表1，支持信息：第1.1节）。270 Mb和269 Mb的N50值表示高连续性，四个最大支架中包含的总装配的95%和96%在大小和数量上与已知的核型相匹配（1n=4，表1）。

The Hi-C contact maps indicate high contiguity in both phases, thus justifying the designation “chromosome-scale” assembly (Fig. 1a). Nevertheless, not all scaffolds are capped by telomere repeats, and 662 and 432 unincorporated contigs remain for S3h1 and S3h2, respectively). The largest fraction of unincorporated contigs comprises various repeat sequences (satellite DNA, telomere repeats, rRNA clusters).

Hi-C接触图表明两个阶段都具有高度的连续性，因此证明了“染色体规模”组装的合理性（图1a）。然而，并非所有支架都被端粒重复序列覆盖，并且S3h1和S3h2分别保留了662和432个未结合的重叠群）。未合并重叠群的最大部分包含各种重复序列（卫星DNA，端粒重复序列，rRNA簇）。

Still, some contigs contain annotated genes (S3h1: 505 genes on 216 contigs, S3h2: 509 genes on 197 contigs), pointing towards remaining localized assembly ambiguities.Table 1 Summary statistics for the genome assemblies and annotations of the four Schmidtea speciesFull size tableFig. 1: Quality control metrics and description of the S.

尽管如此，一些重叠群包含注释基因（216个重叠群上的S3h1:505个基因，197个重叠群上的S3h2:509个基因），指向剩余的局部装配歧义。表1四种Schmidtea物种的基因组组装和注释的汇总统计全尺寸表图。1： 质量控制指标和S的描述。

mediterranea geno.

地中海政策。

Schmidtea mediterranea genome annotation improvementsWe further sought to complement the new genome assembly with high-quality gene annotations. Encountering increasingly diminishing returns on investment with our previous de novo gene prediction approaches42, we developed a new hybrid approach that merges Oxford Nanopore long-reads (ONT), Illumina short-reads, and 3P-seq of transcription termination sites (TTS) data43 with genome-guided transcript assembly, thus leveraging the benefits of direct gene isoform evidence with the base pair accuracy of our genome assembly (Fig. 1f).

Schmidtea mediterranea基因组注释改进我们进一步寻求用高质量的基因注释来补充新的基因组组装。由于我们之前的从头基因预测方法42的投资回报日益减少，我们开发了一种新的混合方法，将牛津纳米孔长读数（ONT），Illumina短读数和3P-seq转录终止位点（TTS）数据43与基因组引导的转录本组装相结合，从而利用直接基因同工型证据的优势和我们基因组组装的碱基对准确性（图1f）。

We generated separate annotation sets for both haplotypes and further designated high-confidence (hconf) transcripts based on Open Reading Frame (ORF) length and/or a minimum coverage threshold (see Methods). With 58,739 and 58,551 gene loci and 21,401 and 21,310 hconf gene loci in S3h1 and S3h2, respectively, these annotations are in range with previous S.

我们根据开放阅读框（ORF）长度和/或最小覆盖阈值（请参见方法），为两种单倍型和进一步指定的高可信度（hconf）转录本生成了单独的注释集。在S3h1和S3h2中分别有58739和58551个基因位点以及21401和21310个hconf基因位点，这些注释与以前的S范围内。

mediterranea gene number estimates26,42,44. To analyze the overall quality of the new annotations, we carried out systematic benchmarking comparisons against previous transcriptomes or S. mediterranea gene model predictions. We first assessed BUSCO representation and completeness. S3BH had the highest number of complete BUSCOs (789) and the fewest missing BUSCOs (134) of all the annotations tested.

地中海基因数量估计26,42,44。为了分析新注释的总体质量，我们对以前的转录组或地中海链球菌基因模型预测进行了系统的基准比较。我们首先评估了BUSCO的代表性和完整性。在所有测试的注释中，S3BH具有最多的完整BUSCO（789）和最少的缺失BUSCO（134）。

Interestingly, the transcriptome or gene model-based BUSCO scores were consistently better than genome-mode BUSCO assessments (Fig. 1g, Supporting Information: Section 1.1), indicating that the detection method used by BUSCO is sub-optimal for planarian genomes. Moreover, the comparatively high number of “missing” BUSCOs reflects a high proportion of genuine gene losses in planarians (see below) and highlights the need for a group-specific BUSCO se.

有趣的是，基于转录组或基因模型的BUSCO评分始终优于基因组模式BUSCO评估（图1g，支持信息：第1.1节），表明BUSCO使用的检测方法对于涡虫基因组来说是次优的。此外，“缺失”的BUSCO数量相对较高，反映了涡虫中真正的基因丢失比例很高（见下文），并突出了对特定群体BUSCO se的需求。

To orthogonally verify our peak annotations, we turned to the principle that the sequences of important regulatory elements are often conserved over evolutionary time51. Since multiple lines of evidence indicate unusually high sequence divergence within planarians and between flatworms in general41,52,53,54,55, we sequenced the genomes of S.

为了正交验证我们的峰注释，我们转向了一个原则，即重要调控元件的序列通常在进化时间内是保守的51。由于多条证据表明涡虫内部和扁虫之间的序列差异异常高[41,52,53,54,55]，我们对S的基因组进行了测序。

mediterranea’s three closest relatives, S. polychroa, S. nova, and S. lugubris (Fig. 3a). All sequenced strains were diploid and displayed the expected karyotypes with 3 or 4 chromosomes56,57,58,59. The Hi-C maps of the assemblies indicated similar scaffolding as for S. mediterranea (Fig. 3b). In addition, the BUSCO scores (Fig. 3c) suggested a comparable completeness to the S.

mediterranea的三个近亲，s.polychroa，s.nova和s.lugubris（图3a）。所有测序的菌株均为二倍体，并显示出预期的核型，具有3或4个染色体56,57,58,59。组件的Hi-C图显示了与S.mediterranea相似的脚手架（图3b）。此外，BUSCO分数（图3c）表明与S相当的完整性。

mediterranea S3 assembly (Fig. 1g). Interestingly, the assemblies of S. nova (1251 Mb) and S. lugubris (1499 Mb) were substantially larger than those of S. mediterranea (840 Mb) and S. polychroa (781 Mb) (Table 1).Fig. 3: Comparative ATAC-seq in the genus Schmidtea to assess regulatory element conservation.a Evolutionary distance of the analyzed Schmidtea species on the basis of 4-fold degenerate sites in the whole genome alignments.

mediterranea S3组件（图1g）。有趣的是，S.nova（1251 Mb）和S.lugubris（1499 Mb）的组装大大大于S.mediterranea（840 Mb）和S.polychroa（781 Mb）（表1）。图3：Schmidtea属的比较ATAC-seq，以评估调控元件的保守性。基于全基因组比对中4倍退化位点，分析的Schmidtea物种的进化距离。

Branch lengths indicate expected substitutions per site. The tree topology is based on a phylogenomic analyses of 930 single-copy genes and agrees with previous work59. b Hi-C contact maps of the genome assemblies of S. polychroa (schPol2), S. nova (schNov1), and S. lugubris (schLug1). c BUSCO completeness assessment of the genome assemblies (left three bars) and the corresponding annotations (right bars) of the new Schmidtea genomes.

分支长度表示每个站点的预期替代。该树拓扑结构基于930个单拷贝基因的系统发育基因组分析，并与以前的工作一致59。b S.polychroa（schPol2），S.nova（schNov1）和S.lugubris（schLug1）基因组组装的Hi-C接触图。。

Since the annotation assessment was run on the transcript level, the “Duplicate” and “Complete” category were combined for the visualization to avoid apparent duplication due to isoforms. d ATAC-seq.

由于注释评估是在转录本级别上进行的，因此将“重复”和“完整”类别结合起来进行可视化，以避免由于同工型而出现明显的重复。d ATAC序列。

Circular consensus sequences from ~30x coverage PacBio reads were called using pbccs (v6.0.0, https://github.com/nlhepler/pbccs) and reads with quality > 0.99 (Q20) were taken forward as “HiFi” reads. Additionally, we generated 1000 million Hi-C reads from extracted nuclei of whole animals using the Arima-HiC+ Kit.

使用pBCC（v6.0.0，https://github.com/nlhepler/pbccs)质量>0.99（Q20）的读数被视为“高保真”读数。此外，我们使用Arima HiC+试剂盒从整个动物的提取细胞核中产生了10亿个Hi-C读数。

PacBio HiFi and Hi-C reads were used to assemble phased contigs with hifiasm (v0.7,94). Next, Hi-C reads whose mapping quality no less than 10 (-q 10) were further utilized to scaffold the contigs from each haplotype by SALSA (v2,95) following the hic-pipeline (https://github.com/esrice/hic-pipeline), which includes filtering procedures such as removal of experimental artifacts from Hi-C alignments, fixing of Hi-C pair mates, and removal of PCR duplicates, etc.

PacBio HiFi和Hi-C读数用于组装具有hifiasm（v0.7,94）的相控重叠群。接下来，进一步利用映射质量不低于10（-q 10）的Hi-C读数，通过SALSA（v2,95）按照hic管道从每个单倍型中构建重叠群(https://github.com/esrice/hic-pipeline)，其中包括过滤程序，例如从Hi-C比对中去除实验伪影，固定Hi-C配对，以及去除PCR重复序列等。

Four chromosome-level scaffolds could be observed in both haplotypes after scaffolding. However, Hi-C heatmap revealed evidence of misplacement of contigs in terms of positions and orientations. These errors were then manually curated based on the interaction frequency indicated by the intensity of Hi-C signals.

支架后，在两种单倍型中都可以观察到四个染色体水平的支架。然而，Hi-C热图揭示了重叠群在位置和方向方面错位的证据。然后根据Hi-C信号强度指示的相互作用频率手动策划这些错误。

To compare the haplotypes with each other and compare them to the schMedS2 assembly, we aligned them using minimap2 (-asm5, v2.24,96) and parsed the alignments using syri (v1.6.3,97).Genome assembly of S. polychroa, S. nova, and S. lugubris.

为了相互比较单倍型并将其与schMedS2组件进行比较，我们使用minimap2（-asm5，v2.24,96）对其进行了比对，并使用syri（v1.6.3,97）对比对进行了分析。S.polychroa，S.nova和S.lugubris的基因组组装。

Circular consensus sequences from PacBio reads were called using pbccs (v6.0.0) and reads with quality > 0.99 (Q20) were taken forward as “HiFi” reads. To create the initial contig assemblies for S. nova, canu v2.1 was used with parameters: maxInputCoverage=100 -pacbio-hifi. For S. polychroa and S. lugubris hifiasm (v0.14.2) was used to create initial contigs with purging parameter: -l 2.

使用pBCC（v6.0.0）调用来自PacBio读物的环状共有序列，并将质量>0.99（Q20）的读物作为“HiFi”读物前进。为了创建S.nova的初始重叠群组件，canu v2.1与参数一起使用：maxInputCoverage=100-pacbio hifi。对于S.polychroa和S.lugubris，使用hifiasm（v0.14.2）创建具有清除参数的初始重叠群：-l 2。

Next, alternative haplotigs were then removed using purge-dups (v1.2.3) using default parameters and cutoff as they were correctly estimated by the program. To initially scaffold the contigs into scaffolds, SALSA v2 (v2.2) was used after mapping Hi-C reads to the contigs. The VGP Arima mapping pipeline was followed: https://github.com/VGP/vgp-assembly/tree/master/pipeline/salsa using bwa-mem (v0.7.17), samtools (v0.10, v1.11) and Picard (v2.22.6).

接下来，使用purge dups（v1.2.3），使用默认参数和截止值删除替代的haplotigs，因为它们是由程序正确估计的。为了最初将重叠群支架到支架中，在将Hi-C读数映射到重叠群后使用SALSA v2（v2.2）。遵循VGP Arima映射管道：https://github.com/VGP/vgp-assembly/tree/master/pipeline/salsa使用bwa mem（v0.7.17）、samtools（v0.10，v1.11）和Picard（v2.22.6）。

False joins in the scaffolds were then broken and missed joins merged manually following the processing of Hi-C reads with pairtools (v0.3.0) and visualization matrices created with cooler (v0.8.11).Following scaffolding, the original PacBio subreads were mapped to the chromosomes using pbmm2 (v1.3.0, https://github.com/PacificBiosciences/pbmm2) with arguments: --preset SUBREAD -N 1 and regions +/− 2 kb around each gap were polished using gcpp’s arrow algorithm (v1.9.0).

然后，在用pairtools（v0.3.0）和用cooler（v0.8.11）创建的可视化矩阵处理Hi-C读数后，支架中的假连接被破坏，错过的连接被手动合并。搭建支架后，使用pbmm2（v1.3.0，https://github.com/PacificBiosciences/pbmm2)带有参数：-使用gcpp的箭头算法（v1.9.0）对每个间隙周围的预设子读数N 1和+/-2 kb区域进行了抛光。

Those regions in which gaps were closed and polished with all capital nucleotides (gcpp’s internal high confidence threshold) were then inserted into the assemblies as closed gaps.Lastly, the PacBio HiFi (CCS reads with a read quality exceeding 0.99) were aligned to the genomes using pbmm2 (v1.3.0) with the arguments --preset CCS -N 1.

然后将间隙封闭并用所有资本核苷酸（gcpp的内部高可信度阈值）抛光的区域作为闭合间隙插入组件中。最后，使用pbmm2（v1.3.0）将PacBio HiFi（读取质量超过0.99的CCS读取）与基因组进行比对，参数为预设CCS-N 1。

DeepVariant (v1.2.0,98) was used to detect variants in the alignments to the assembled sequence. Only the homozygous variants (GT = 1/1) that .

。只有纯合子变体（GT = 1/1）才能。

Data availability

数据可用性

The whole-genome, Hi-C, ATAC-seq, ChIP-seq, and RNA-Seq of Schmidtea mediterranea, Schmidtea polychroa, Schmidtea nova, and Schmidtea lugubris data generated in this study have been deposited in the NCBI database under accession code PRJNA1052007. The repetitive element annotation of Schmidtea genomes data generated in this study have been deposited in the Zenodo database under accession code 11004547.

本研究中产生的Schmidtea mediterranea，Schmidtea polychroa，Schmidtea nova和Schmidtea lugubris数据的全基因组，Hi-C，ATAC-seq，ChIP-seq和RNA-seq已保存在NCBI数据库中，登录号为PRJNA105207。本研究中产生的Schmidtea基因组数据的重复元素注释已保存在Zenodo数据库中，登录号为11004547。

The Clonorchis sinensis genome and annotation data used in this study are available in the NCBI database under accession code PRJNA386618. The Schistosoma mansoni genome and annotation data used in this study are available in the NCBI database under accession code PRJEA36577. The Taenia multiceps genome and annotation data used in this study are available in the NCBI database under accession code PRJNA307624.

本研究中使用的华支睾吸虫基因组和注释数据可在NCBI数据库中获得，登录号为PRJNA386618。本研究中使用的曼氏血吸虫基因组和注释数据可在NCBI数据库中获得，登录号为PRJEA36577。本研究中使用的多头绦虫基因组和注释数据可在NCBI数据库中获得，登录号为PRJNA307624。

The Hymenolepis microstoma genome and annotation data used in this study are available in the NCBI database under accession code PRJEB124. The Macrostomum hystrix gene annotation data used in this study are available in the Zenodo database under accession code 7861770. The Macrostomum hystrix genome data used in this study are available in the European Nucleotide Archive database under accession code GCA_950097015. Source data are provided with this paper..

本研究中使用的膜翅目微瘤基因组和注释数据可在NCBI数据库中以登录号PRJEB124获得。本研究中使用的Macrostomum hystrix基因注释数据可在Zenodo数据库中获得，登录号为7861770。本研究中使用的Macrostomum hystrix基因组数据可在欧洲核苷酸档案数据库中获得，登录号为GCA\U 950097015。本文提供了源数据。。

Code availability

代码可用性

The code used to conduct the analysis in this study is available at https://github.com/Jeremias-Brand/PlanarianGenomeAnalysis and has been archived in the Zenodo database under accession code 13123038.

本研究中用于进行分析的代码可在https://github.com/Jeremias-Brand/PlanarianGenomeAnalysis并已在Zenodo数据库中存档，登录号为13123038。

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Download referencesAcknowledgementsWe thank Heino Andreas, Rick Kluivert, Jens Krull, and the MPI-NAT animal services staff for worm care and the maintenance of the species collection. We thank Tobias Boothe for picture acquisition. We thank Juliana G. Roscito for sequencing support and close collaboration during method development.

下载参考文献致谢我们感谢Heino Andreas，Rick Kluivert，Jens Krull和MPI-NAT动物服务人员对蠕虫的护理和物种收集的维护。我们感谢Tobias Boothe的图片采集。我们感谢Juliana G.Roscito在方法开发过程中提供的测序支持和密切合作。

We thank Hanh Vu for access to S. mediterranea RNA-seq data. We thank the following facilities for their support: the DRESDEN Concept Genome Center, part of the MPI-CBG and the technology platform of the CMCB at the TU Dresden, supported by DFG (INST 269/768-1); the Genomics Core Facility of the European Molecular Biology Laboratory in Heidelberg; and the IIT Genomics Facility.

我们感谢Hanh Vu访问S.mediterranea RNA-seq数据。我们感谢以下设施的支持：德累斯顿概念基因组中心（MPI-CBG的一部分）和德累斯顿大学CMCB的技术平台，由DFG（INST 269/768-1）支持；海德堡欧洲分子生物学实验室基因组学核心设施；和IIT基因组学设施。

We are grateful to Diego Vozzi, Yeraldin Castillo Spelorzi, and Edoardo Henzen for their technical support of the Nanopore sequencing experiments. JCR received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement number 649024), from the German Research Foundation (project RI 2449/51), from the Behrens-Weise Foundation, and from the Max Planck Society.

我们感谢Diego Vozzi，Yeraldin Castillo Spelorzi和Edoardo Henzen对纳米孔测序实验的技术支持。JCR获得了欧盟地平线2020研究与创新计划（授权协议号649024）下欧洲研究理事会（ERC）的资助，德国研究基金会（RI 2449/51项目），贝伦斯·韦斯基金会和马克斯·普朗克学会的资助。

JNB was supported by Swiss National Science Foundation Grant P500PB_206673. LP, AC and SG were supported by intramural funding of the Istituto Italiano di Tecnologia. AP was supported by the SPP2202 Priority program (Project No. 422389065).FundingOpen Access funding enabled and organized by Projekt DEAL.Author informationAuthor notesThese authors contributed equally: Mario Ivanković, Jeremias N.

。LP、AC和SG得到了意大利技术研究所（Istituto Italiano di Tecnologia）的校内资助。AP得到了SPP2202优先项目（项目编号422389065）的支持。资金开放获取资金由Projekt交易启用和组织。作者信息作者注意到这些作者做出了同样的贡献：Mario Ivanković，Jeremias N。

Brand.Authors and AffiliationsDepartment of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, GermanyMario Ivanković, Jeremias N. Brand, Andrei Rozanski, Til Schubert, Miquel Vila-F.

品牌。作者和附属机构马克斯·普朗克多学科科学研究所组织动力学与再生系，哥廷根，GermanyMario Ivanković，Jeremias N.Brand，Andrei Rozanski，Til Schubert，Miquel Vila-F。

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PubMed Google ScholarContributionsM.I., J.N.B, and J.C.R designed the study and wrote the manuscript. T.B., M.P., M.Z., and A.M. performed genome assembly. L.P., A.R., L. R., and J.N.B performed genome annotation. T.S. and M.A.G. developed and applied DNA extraction protocols.

PubMed谷歌学术贡献。一、 ，J.N.B和J.C.R设计了这项研究并撰写了手稿。T、 B.，M.P.，M.Z。和A.M.进行了基因组组装。五十、 P.，A.R.，L.R。和J.N.B进行了基因组注释。T、 。

M.I. designed, developed, performed, and analyzed ATAC-seq and ChIP-seq experiments. S.W. performed method development and application of HiFi sequencing. M.I. performed Hi-C experiments. S.Z. and A.P. supported and performed some of the Hi-C experiments. L.P., A.C., and S.G. performed nanopore sequencing.

M、 I.设计，开发，执行和分析ATAC-seq和ChIP-seq实验。S、 W.进行了高保真测序的方法开发和应用。M、 I.进行了Hi-C实验。S、 Z.和A.P.支持并执行了一些Hi-C实验。五十、 P.，A.C。和S.G.进行了纳米孔测序。

M.V.F. and J.C.R. collected and identified S. nova, S. polychroa, and S. lugubris. J.N.B. performed genome alignment, phylogenetics, and comparative genomics analyses. J.C.R. received funding and supervised the research.Corresponding authorCorrespondence to.

M、 V.F.和J.C.R.收集并鉴定了S.nova，S.polychroa和S.lugubris。J.N.B.进行了基因组比对，系统发育和比较基因组学分析。J、 C.R.获得了资金并监督了这项研究。对应作者对应。

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Reprints and permissionsAbout this articleCite this articleIvanković, M., Brand, J.N., Pandolfini, L. et al. A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.

转载和许可本文引用本文Ivanković，M.，Brand，J.N.，Pandolfini，L。等人。对涡虫基因组的比较分析揭示了面对快速结构分化的监管保守性。

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