Phoronid genome supports a monophyletic Lophophorata

Resolving deep branches of the animal tree of life remains a major challenge in evolutionary biology. One long-standing debate concerns the clade Lophophorata, which includes brachiopods, phoronids, and bryozoans, united by a ciliated feeding organ known as the lophophore. While some phylogenomic studies support lophophorate monophyly, others group bryozoans with entoprocts and cycliophorans as Polyzoa. Here, we show that shared chromosome fusion events provide sequence-independent evidence for a sister relationship between phoronids and bryozoans. Using a new chromosome-level genome of a phoronid, we identify seven irreversible fusion-with-mixing events shared with bryozoans, one of which is also found in brachiopods. These fusions are absent from other lophotrochozoans, including molluscs, annelids, and nemerteans, supporting the monophyly of Lophophorata. This structural evidence is independently corroborated by phylogenomic analyses of orthologs with reliable phylogenetic signals, which likewise recover Lophophorata as a monophyletic group. Transcriptomic profiling of lophophores across the three lophophorate phyla reveals conserved expression of vertebrate head and neural developmental genes, providing molecular evidence that these structures are homologous organs rather than convergent adaptations for filter feeding. Together, these findings robustly place phoronids with bryozoans, support the homology of lophophores, resolve a century-old debate in metazoan phylogeny, and underscore the power of genome structure and tissue transcriptomics in reconstructing deep evolutionary relationships. This project includes a chromosome-level genome assembly and gene models for the phoronid Phoronis australis, gene models for the brachiopod Lingula anatina, and a transcriptome assembly for the bryozoan Flustrellidra hispida. It also includes de novo transcriptome assemblies generated from publicly available NCBI SRA data for the phoronid Phoronopsis harmeri (SRR2131255), the brachiopods Novocrania anomala (SRR2681681) and Terebratalia transversa (SRR2005824), and the cycliophoran Symbion pandora (SRR3102772). Gene expression matrices across multiple tissues, along with functional annotations, are provided for L. anatina, P. australis, and F. hispida. Phoronis australis – genome assembly, gene models, expression matrix, and annotations: - Genome_assembly: Phoronis_australis.fasta - Gene_models: Phoronis_australis.gtf - CDS_nucleotide: Phoronis_australis.fna - CDS_protein: Phoronis_australis.faa - Gene_expression: Phoronis_australis.salmon.isoform.TMM.EXPR.matrix - Annotation_eggnog_mapper: Phoronis_australis.annotation.eggnog_mapper - Annotation_uniprot_sprot: Phoronis_australis.annotation.uniprot_sprot.diamond_blastp Lingula anatina – gene models, expression matrix, and annotations: - CDS_nucleotide: Lingula_anatina.fna - CDS_protein: Lingula_anatina.faa - Gene_expression: Lingula_anatina.salmon.isoform.TMM.EXPR.matrix - Annotation_eggnog_mapper: Lingula_anatina.annotation.eggnog_mapper - Annotation_uniprot_sprot: Lingula_anatina.annotation.uniprot_sprot.diamond_blastp Flustrellidra hispida – transcriptome assembly, expression matrix, and annotations: - CDS_nucleotide: Flustrellidra_hispida.fna - CDS_protein: Flustrellidra_hispida.faa - Gene_expression: Flustrellidra_hispida.salmon.isoform.TMM.EXPR.matrix - Annotation_eggnog_mapper: Flustrellidra_hispida.annotation.eggnog_mapper - Annotation_uniprot_sprot: Flustrellidra_hispida.annotation.uniprot_sprot.diamond_blastp Transcriptome assemblies from public SRA datasets (de novo assembled in this study): Novocrania anomala (SRA: SRR2681681) - CDS_nucleotide: Novocrania_anomala.fna - CDS_protein: Novocrania_anomala.faa Terebratalia transversa (SRA: SRR2005824) - CDS_nucleotide: Terebratalia_transversa.fna - CDS_protein: Terebratalia_transversa.faa Phoronopsis harmeri (SRA: SRR2131255) - CDS_nucleotide: Phoronopsis_harmeri.fna - CDS_protein: Phoronopsis_harmeri.faa Symbion pandora (SRA: SRR3102772) - CDS_nucleotide: Symbion_pandora.fna - CDS_protein: Symbion_pandora.faa