{"doi":"10.3390/ani15243526","title":"Complete Mitochondrial Genomes of Pentapodus caninus and Lethrinus olivaceus (Spariformes: Nemipteridae and Lethrinidae): Genome Characterization and Phylogenetic Analysis","abstract":"Complete mitochondrial genomes (mitogenomes) are widely utilized molecular resources for phylogenetic studies. Although research on Spariformes mitogenomes has advanced significantly, there is still relatively little information regarding the molecular data and taxonomic placement of the families Nemipteridae and Lethrinidae. We report and annotate the first complete mitogenomes of Pentapodus caninus (16,866 bp; Nemipteridae) and Lethrinus olivaceus (16,792 bp; Lethrinidae), thereby expanding mitogenomic coverage in two families with limited available genomic data. Both assembled mitogenomes display the canonical vertebrate architecture, comprising 37 functional genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region, with conserved synteny and strand asymmetry (only ND6 and eight tRNAs are light-strand encoded). While ATG serves as the primary initiation codon for most PCGs, COX1 employs an alternative GTG start codon. Structural analysis of tRNAs revealed that most sequences adopt the standard cloverleaf conformation, with the exception of tRNA-SerAGY, which lacks the dihydrouridine (DHU) arm. A rare tandem duplication of tRNA-Val in Lethrinus species highlights the structural variability of spariform mitochondrial genomes. Furthermore, phylogenomic reconstruction using the concatenated 13 protein-coding gene dataset recovered Nemipteridae and Sparidae as sister taxa. In this topology, Lethrinidae was identified as the earliest diverging lineage, basal to the Nemipteridae–Sparidae grouping. Our results not only advance our understanding of the origin and evolution of Spariformes, but also provide valuable information for the molecular phylogeny and taxonomy of teleostean species.","journal":"Animals","year":2025,"id":584489,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9017,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":56.25,"fair_percentile":71.90461632528279,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1497675,"name":"Mingcan Gu","orcid":null,"position":1,"is_corresponding":false},{"id":1497276,"name":"Wenqing Jiang","orcid":"0000-0003-4955-2503","position":2,"is_corresponding":false},{"id":1497277,"name":"Lei Xie","orcid":"0000-0002-8883-950X","position":3,"is_corresponding":false},{"id":1497278,"name":"Q. Y. Qiao","orcid":"0000-0002-9848-3180","position":4,"is_corresponding":false},{"id":1497676,"name":"Jingyi Cen","orcid":null,"position":5,"is_corresponding":false},{"id":1497279,"name":"Yuelei Dong","orcid":"0009-0007-3052-6686","position":6,"is_corresponding":false},{"id":1497280,"name":"Songhui Lü","orcid":"0000-0002-7514-6501","position":7,"is_corresponding":false},{"id":1468098,"name":"Lei Cui","orcid":"0000-0003-4365-5173","position":8,"is_corresponding":false},{"id":1497275,"name":"Nan Chen","orcid":"0000-0001-6851-5658","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-19T02:59:11.978098Z","pmid":"41463811","pmcid":"PMC12729901","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":83.3333,"fair_a":62.5,"fair_i":0.0,"fair_r":29.1667,"fair_zscore":0.8629,"fair_rationale":{"fair_score":56.25,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The newly obtained mitogenome sequences of the P. caninus and L. olivaceus were submitted to the GenBank database under the accession number PV872034 and PV872036 , respectively.","grounded":true,"rationale":"The paper provides GenBank accession numbers, which are persistent identifier strings. 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[majority verdict 'no' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community data or metadata standard (e.g., MIAME, MIxS, FAIRsharing-registered ontology) is named for the data.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"Perca fluviatilis (NC_026313) and Epinephelus coioides (NC_011111)","grounded":false,"rationale":"The paper includes GenBank accessions for other species' mitogenomes used in the analysis. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license artefact is named for the data; the article's CC BY license applies to the paper, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. 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[majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. 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A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:51:11.949769Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}