{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T12:45:32Z","timestamp":1763037932365,"version":"3.37.3"},"reference-count":40,"publisher":"Cambridge University Press (CUP)","issue":"3","license":[{"start":{"date-parts":[[2024,1,15]],"date-time":"2024-01-15T00:00:00Z","timestamp":1705276800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","award":["A1-S-21694"],"award-info":[{"award-number":["A1-S-21694"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006087","name":"Direcci\u00f3n General de Asuntos del Personal Acad\u00e9mico, Universidad Nacional Aut\u00f3noma de M\u00e9xico","doi-asserted-by":"publisher","award":["IN212621"],"award-info":[{"award-number":["IN212621"]}],"id":[{"id":"10.13039\/501100006087","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Parasitology"],"published-print":{"date-parts":[[2024,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Trematodes of the family Allocreadiidae are primarily found in the intestines of freshwater fishes around the world. The family includes 15 genera and c. 130 species. The last 2 decades have witnessed an increase in the genetic library of its species. Molecular data have been crucial for species delimitation and species description within Allocreadiidae and for understanding their evolutionary and biogeographical history and classification. Here, the mitogenomes of 3 species of allocreadiids were obtained using high throughput sequencing methods. Mitogenomes were compared with other members of the order Plagiorchiida to determine their molecular composition, gene rearrangement and phylogenetic interrelationships. The complete circular mitogenomes of <jats:italic>Allocreadium lobatum, Creptotrematina aguirrepequenoi<\/jats:italic> and <jats:italic>Wallinia mexicana<\/jats:italic> were 14 424, 13 769 and 13 924 bp long respectively, comprising 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. Gene arrangements were identical to other Xiphidiatan trematodes. Phylogenetic analyses using the mitogenomes revealed Allocreadiidae as a monophyletic group closely related to other members of the suborder Xiphidiata; <jats:italic>A. lobatum<\/jats:italic> was yielded as the sister taxon of <jats:italic>C. aguirrepequenoi<\/jats:italic> + <jats:italic>W. mexicana<\/jats:italic>. Our study increases the complete mitochondrial genome library of trematodes and strengthens our understanding of the phylogenetic relationships and classification of this parasite group.<\/jats:p>","DOI":"10.1017\/s0031182024000064","type":"journal-article","created":{"date-parts":[[2024,1,15]],"date-time":"2024-01-15T09:45:30Z","timestamp":1705311930000},"page":"309-318","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":8,"title":["The complete mitochondrial genome of 3 species of allocreadiids (Digenea, Allocreadiidae): characterization and phylogenetic position within the order Plagiorchiida"],"prefix":"10.1017","volume":"151","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6367-477X","authenticated-orcid":false,"given":"Brenda","family":"Sol\u00f3rzano-Garc\u00eda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0822-3498","authenticated-orcid":false,"given":"David I.","family":"Hern\u00e1ndez-Mena","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7553-4179","authenticated-orcid":false,"given":"Anindo","family":"Choudhury","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6472-5113","authenticated-orcid":false,"given":"Gerardo","family":"P\u00e9rez-Ponce de Le\u00f3n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"56","published-online":{"date-parts":[[2024,1,15]]},"reference":[{"key":"S0031182024000064_ref7","first-page":"417","volume-title":"Keys to the Trematoda","volume":"2","author":"Caira","year":"2005"},{"key":"S0031182024000064_ref19","doi-asserted-by":"crossref","first-page":"596914","DOI":"10.3389\/fmicb.2020.596914","article-title":"Naturally occurring tRNAs with non-canonical structures","volume":"11","author":"Krahn","year":"2020","journal-title":"Frontiers in Microbiology"},{"key":"S0031182024000064_ref8","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.gene.2015.09.081","article-title":"Sequencing and characterization of the complete mitochondrial genome from the pancreatic fluke Eurytrema pancreaticum (Trematoda: Dicrocoeliidae)","volume":"2016","author":"Chang","year":"2016","journal-title":"Gene"},{"key":"S0031182024000064_ref23","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.ympev.2005.12.012","article-title":"The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms","volume":"39","author":"Littlewood","year":"2006","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"S0031182024000064_ref25","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"key":"S0031182024000064_ref29","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1645\/15-815","article-title":"Phylogenetic analysis using the 28S rRNA gene reveals that the genus Paracreptotrema (Digenea: Allocreadiidae) is not monophyletic: description of two new genera and one new species","volume":"102","author":"P\u00e9rez-Ponce de Le\u00f3n","year":"2016","journal-title":"Journal of Parasitology"},{"key":"S0031182024000064_ref6","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.parint.2016.02.004","article-title":"The mitochondrial genome and ribosomal operon of Brachycladium goliath (Digenea: Brachycladiidae) recovered from a stranded minke whale","volume":"65","author":"Briscoe","year":"2016","journal-title":"Parasitology International"},{"key":"S0031182024000064_ref35","first-page":"1312","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"key":"S0031182024000064_ref36","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.parint.2019.04.001","article-title":"Characterization of the complete mitochondrial genome of Plagiorchis maculosus (Digenea, Plagiorchiidae), Representative of a taxonomically complex digenean family","volume":"71","author":"Suleman","year":"2019","journal-title":"Parasitology International"},{"key":"S0031182024000064_ref39","doi-asserted-by":"crossref","first-page":"102412","DOI":"10.1016\/j.parint.2021.102412","article-title":"Systematics of Crepidostomum species from the Russian Far East and northern Japan, with description of a new species and validation of the genus Stephanophiala","volume":"84","author":"Vainutis","year":"2021","journal-title":"Parasitology International"},{"key":"S0031182024000064_ref21","first-page":"172","article-title":"ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences","volume":"24","author":"Laslett","year":"2008","journal-title":"Bioinformatics (Oxford, England)"},{"key":"S0031182024000064_ref33","doi-asserted-by":"crossref","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP 6: DNA sequence polymorphism analysis of large data sets","volume":"34","author":"Rozas","year":"2017","journal-title":"Molecular Biology Evolution"},{"key":"S0031182024000064_ref15","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1051\/parasite\/2021065","article-title":"Three new species of Creptotrema (Trematoda, Allocreadiidae) with an amended diagnosis of the genus and reassignment of Auriculostoma (Allocreadiidae), based on morphological and molecular evidence","volume":"28","author":"Franceschini","year":"2021","journal-title":"Parasite"},{"key":"S0031182024000064_ref13","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1645\/GE-2641.1","article-title":"Phylogenetic affinities of Auriculostoma (Digenea: Allocreadiidae), with descriptions of two new species from Peru","volume":"97","author":"Curran","year":"2011","journal-title":"Journal of Parasitology"},{"key":"S0031182024000064_ref34","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1007\/s00436-023-07893-5","article-title":"Phylogenetic assessment of some Palearctic Allocreadium spp. (Trematoda, Gorgoderoidea: Allocreadiidae)","volume":"122","author":"Sokolov","year":"2023","journal-title":"Parasitology Research"},{"key":"S0031182024000064_ref38","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s13071-020-04547-8","article-title":"Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications","volume":"14","author":"Suleman","year":"2021","journal-title":"Parasites and Vectors"},{"key":"S0031182024000064_ref28","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/s11230-006-9081-3","article-title":"The systematic position of Wallinia spp. and Margotrema spp. (Digenea), parasites of Middle-American and Neotropical freshwater fishes, based on the 28S ribosomal RNA gene","volume":"68","author":"P\u00e9rez-Ponce de Le\u00f3n","year":"2007","journal-title":"Systematic Parasitology"},{"key":"S0031182024000064_ref22","doi-asserted-by":"crossref","first-page":"e7031","DOI":"10.7717\/peerj.7031","article-title":"The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes","volume":"7","author":"Le","year":"2019","journal-title":"PeerJ"},{"key":"S0031182024000064_ref30","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1017\/S0022149X2000053X","article-title":"Disentangling the evolutionary and biogeographical history of the freshwater fish trematode genus Creptotrema (Digenea: Allocreadiidae) using an integrative taxonomy approach: the case of Creptotrema agonostomi in Middle American mountain mullets","volume":"94","author":"P\u00e9rez-Ponce de Le\u00f3n","year":"2020","journal-title":"Journal of Helminthology"},{"key":"S0031182024000064_ref11","first-page":"861","article-title":"GenomeVx: simple web-based creation of editable circular chromosome maps","volume":"24","author":"Conant","year":"2008","journal-title":"Bioinformatics (Oxford, England)"},{"key":"S0031182024000064_ref20","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Molecular Biology and Evolution"},{"key":"S0031182024000064_ref2","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s11230-020-09901-z","article-title":"Amended diagnosis, validity and relationships of the genus Acrolichanus Ward, 1917 (Digenea: Allocreadiidae) based on the 28S rRNA gene, and observations on its lineage diversity","volume":"97","author":"Atopkin","year":"2020","journal-title":"Systematic Parasitology"},{"key":"S0031182024000064_ref40","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s11230-022-10081-1","article-title":"Integrative approach for discovering of the new species within the genus Allocreadium Looss, 1900 (Trematoda: Allocreadiidae) and framing of biogeographical hypotheses for the genus","volume":"100","author":"Vainutis","year":"2023","journal-title":"Systematic Parasitology"},{"key":"S0031182024000064_ref31","doi-asserted-by":"crossref","first-page":"645","DOI":"10.3390\/d15050645","article-title":"Hidden diversity in European Allocreadium spp. (Trematoda, Allocreadiidae) and the discovery of the adult stage of Cercariaeum crassum Wesenberg-Lund, 1934","volume":"15","author":"Petkevi\u010di\u016bt\u0117","year":"2023","journal-title":"Diversity"},{"key":"S0031182024000064_ref1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.ijppaw.2022.07.009","article-title":"Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication","volume":"19","author":"An","year":"2022","journal-title":"International Journal for Parasitology \u2013 Parasites and Wildlife"},{"key":"S0031182024000064_ref14","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1007\/s00436-020-06724-1","article-title":"Unexpected diversity in Northern Europe: trematodes from salmonid fishes in Iceland with two new species of Crepidostomum Braun, 1900","volume":"119","author":"Falt\u00fdnkov\u00e1","year":"2020","journal-title":"Parasitology Ressearch"},{"key":"S0031182024000064_ref32","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1080\/23802359.2018.1462119","article-title":"Characterization of the complete mitochondrial genome of the lung fluke, Paragonimus heterotremus","volume":"3","author":"Qian","year":"2018","journal-title":"Mitochondrial Dna Part B: Resources"},{"key":"S0031182024000064_ref4","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.ympev.2012.08.023","article-title":"MITOS: improved de novo metazoan mitochondrial genome annotation","volume":"69","author":"Bernt","year":"2013","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"S0031182024000064_ref17","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1645\/GE-523R.1","article-title":"Phylogenetic relationships of Palaeacanthocephala (Acanthocephala) inferred from SSU and LSU rRNA gene sequences","volume":"91","author":"Garc\u00eda-Varela","year":"2005","journal-title":"Journal of Parasitology"},{"key":"S0031182024000064_ref24","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.ympev.2014.07.002","article-title":"Dicrocoelium chinensis and Dicrocoelium dendriticum (Trematoda: Digenea) are distinct lancet fluke species based on mitochondrial and nuclear ribosomal DNA sequences","volume":"79","author":"Liu","year":"2014","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"S0031182024000064_ref27","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1017\/S0022149X19000191","article-title":"Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the \u2018next-generation\u2019 Tree of Life","volume":"93","author":"P\u00e9rez-Ponce de Le\u00f3n","year":"2019","journal-title":"Journal of Helminthology"},{"key":"S0031182024000064_ref37","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/s13071-020-3940-7","article-title":"Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea:Dicrocoeliidae) and comparison with mammalian dicrocoeliids","volume":"13","author":"Suleman","year":"2020","journal-title":"Parasites and Vectors"},{"key":"S0031182024000064_ref16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S0031182023000379","article-title":"The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications","volume":"150","author":"Gao","year":"2023","journal-title":"Parasitology"},{"key":"S0031182024000064_ref18","doi-asserted-by":"crossref","first-page":"106469","DOI":"10.1016\/j.actatropica.2022.106469","article-title":"The complete mitochondrial genome of Prosthogonimus cuneatus and Prosthogonimus pellucidus (Trematoda: Prosthogonimidae), their features and phylogenetic relationships in the superfamily Microphalloidea","volume":"232","author":"Guo","year":"2022","journal-title":"Acta Tropica"},{"key":"S0031182024000064_ref12","doi-asserted-by":"crossref","first-page":"238","DOI":"10.2478\/s11686-006-0037-1","article-title":"A review of Polylekithum Arnold, 1934 and its familial affinities using morpho logical and molecular data, with description of Polylekithum catahoulensis sp. nov","volume":"51","author":"Curran","year":"2006","journal-title":"Acta Parasitologica"},{"key":"S0031182024000064_ref3","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1017\/S0022149X23000500","article-title":"A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences","volume":"97","author":"Atopkin","year":"2023","journal-title":"Journal of Helminthology"},{"key":"S0031182024000064_ref26","doi-asserted-by":"crossref","first-page":"284","DOI":"10.2478\/helm-2022-0029","article-title":"Discovery of a new genus and species of Allocreadiidae (Trematoda) in Mexico: Mesoamericatrema magnisacculus n. gen. n. sp","volume":"59","author":"Mendoza-Garfias","year":"2022","journal-title":"Helminthologia"},{"key":"S0031182024000064_ref10","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1645\/GE-966R.1","article-title":"The phylogenetic position of Allocreadiidae (Trematoda: Digenea) from partial sequences of the 18S and 28S ribosomal RNA genes","volume":"93","author":"Choudhury","year":"2007","journal-title":"Journal of Parasitology"},{"key":"S0031182024000064_ref9","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1645\/GE-3540.1","article-title":"Paracreptotrema blancoi n. gen. n. sp. (Digenea: Plagiorchiformes: Allocreadiidae) in the olomina, Priapichthys annectens (Osteichthyes: Poeciliidae) from the \u00c1rea de Conservaci\u00f3n Guanacaste, Costa Rica","volume":"92","author":"Choudhury","year":"2006","journal-title":"Journal of Parasitology"},{"key":"S0031182024000064_ref5","doi-asserted-by":"crossref","first-page":"e484","DOI":"10.7717\/peerj.484","article-title":"The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)","volume":"12","author":"Biswal","year":"2014","journal-title":"Peerj"}],"container-title":["Parasitology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0031182024000064","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T10:29:24Z","timestamp":1712572164000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0031182024000064\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,15]]},"references-count":40,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3]]}},"alternative-id":["S0031182024000064"],"URL":"https:\/\/doi.org\/10.1017\/s0031182024000064","relation":{},"ISSN":["0031-1820","1469-8161"],"issn-type":[{"type":"print","value":"0031-1820"},{"type":"electronic","value":"1469-8161"}],"subject":[],"published":{"date-parts":[[2024,1,15]]},"assertion":[{"value":"Copyright \u00a9 The Author(s), 2024. Published by Cambridge University Press","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http:\/\/creativecommons.org\/licenses\/by\/4.0\/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}