{"doi":"10.1111/zsc.70056","title":"Progress and Challenges in Phylogenomics and Genomics of Lophotrochozoa/Spiralia","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>Lophotrochozoa is one of the three major bilaterian groups comprising more than half of the bilaterian phyla. Lophotrochozoa includes among others Mollusca, Annelida, Platyhelminthes and Rotifera. Despite representing such a large proportion of animal diversity, they are historically understudied and genomic resources have been scarce. However, the last years have seen a strong increase of genomic resources due to the initiatives associated with the Earth Biogenome Project. Hence, herein I will review the progress made with respect to the available genomic resources for Lophotrochozoa and its phylogeny based on genome‐scale data. With several hundreds of chromosome‐level genomes available for Lophotrochozoa, tremendous progress has been achieved. However, tissue availability in relation to the genome size remains a major challenge and genomic information for small‐sized lophotrochozoan taxa like Gnathostomulida and Entoprocta are still missing on a large scale. Hence, a major challenge remains to obtain enough high‐quality DNA despite recent progresses in whole‐genome amplification methods. Summarizing recent phylogenomic studies showed that monophyletic Chaetognathifera is sister to the remaining Lophotrochozoa, known as Platytrochozoa. Within Platytrochozoa, Rouphozoa, Entoprocta + Cycliophora, Lophophorata and Bryozoa + Phoronida can be recognized as monophyletic, but other relationships are contentious. Moreover, to date, no phylogenomic study has sampled all lophotrochozoan phyla. Reviewing macrosyntenic studies and patterns across Lophotrochozoa reveals that its potential as a phylogenetic marker might be much more limited than expected. The analyses show very high degrees of convergent evolution, in part due to massive fusion events. Hence, convergent evolution of fusion‐with‐mixing events might be more rampant than assumed at present.</jats:p>","journal":"Zoologica Scripta","year":2026,"id":631768,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1637347,"name":"Torsten H. Struck","orcid":"0000-0003-3280-6239","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Progress and Challenges in Phylogenomics and Genomics of Lophotrochozoa/Spiralia","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>Lophotrochozoa is one of the three major bilaterian groups comprising more than half of the bilaterian phyla. Lophotrochozoa includes among others Mollusca, Annelida, Platyhelminthes and Rotifera. Despite representing such a large proportion of animal diversity, they are historically understudied and genomic resources have been scarce. However, the last years have seen a strong increase of genomic resources due to the initiatives associated with the Earth Biogenome Project. Hence, herein I will review the progress made with respect to the available genomic resources for Lophotrochozoa and its phylogeny based on genome‐scale data. With several hundreds of chromosome‐level genomes available for Lophotrochozoa, tremendous progress has been achieved. However, tissue availability in relation to the genome size remains a major challenge and genomic information for small‐sized lophotrochozoan taxa like Gnathostomulida and Entoprocta are still missing on a large scale. Hence, a major challenge remains to obtain enough high‐quality DNA despite recent progresses in whole‐genome amplification methods. Summarizing recent phylogenomic studies showed that monophyletic Chaetognathifera is sister to the remaining Lophotrochozoa, known as Platytrochozoa. Within Platytrochozoa, Rouphozoa, Entoprocta + Cycliophora, Lophophorata and Bryozoa + Phoronida can be recognized as monophyletic, but other relationships are contentious. Moreover, to date, no phylogenomic study has sampled all lophotrochozoan phyla. Reviewing macrosyntenic studies and patterns across Lophotrochozoa reveals that its potential as a phylogenetic marker might be much more limited than expected. The analyses show very high degrees of convergent evolution, in part due to massive fusion events. Hence, convergent evolution of fusion‐with‐mixing events might be more rampant than assumed at present.</jats:p>","is_dataset_classified":null,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19767382","pmcid":null,"openalex_id":"https://openalex.org/W7149490995","authors":[],"funders":[{"funder_name":"Norges Forskningsråd","grant_id":"300587","title":"InvertOmics - Phylogeny and evolution of lophotrochozoan invertebrates based on genomic data"}],"total_grants":1,"fwci":8.5721,"citation_percentile":0.96688104,"influential_citations":0,"citation_trend":[{"year":2026,"count":1}],"oa_status":"hybrid","license":"cc-by-nc-nd","oa_locations":[{"url":"https://doi.org/10.1111/zsc.70056","host_type":"journal"},{"url":"https://doi.org/10.1111/zsc.70056","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/zsc.70056","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/zsc.70056","host_type":"publisher"}],"fields_of_study":["Marine Ecology and Invasive Species","Protist diversity and phylogeny","Marine Biology and Ecology Research","0106 biological sciences","01 natural sciences"],"mesh_terms":[],"keywords":["Phylogenomics","Phylogenetics","Genomics","Convergent evolution","Phylogenetic tree","Genome","Comparative genomics"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T00:38:50.877294Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}