{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T17:39:09Z","timestamp":1787593149394,"version":"build-2736575974"},"reference-count":72,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T00:00:00Z","timestamp":1701216000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["21-74-20028"],"award-info":[{"award-number":["21-74-20028"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three \u201cORFan\u201d regions (544, 1,060, and 427\u2005bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora\/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.<\/jats:p>","DOI":"10.1093\/gbe\/evad219","type":"journal-article","created":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T16:59:16Z","timestamp":1701277156000},"source":"Crossref","is-referenced-by-count":6,"title":["ORFans in Mitochondrial Genomes of Marine Polychaete <i>Polydora<\/i>"],"prefix":"10.1093","volume":"15","author":[{"given":"Maria","family":"Selifanova","sequence":"first","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oleg","family":"Demianchenko","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2835-3708","authenticated-orcid":false,"given":"Elizaveta","family":"Noskova","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Egor","family":"Pitikov","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denis","family":"Skvortsov","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Drozd","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nika","family":"Vatolkina","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Polina","family":"Apel","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina","family":"Kolodyazhnaya","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarita A","family":"Ezhova","sequence":"additional","affiliation":[{"name":"Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University , Moscow , Russia"},{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander B","family":"Tzetlin","sequence":"additional","affiliation":[{"name":"Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana V","family":"Neretina","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow , Russia"},{"name":"Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University , Moscow , Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) , Russian Academy of Science, Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7468-6963","authenticated-orcid":false,"given":"Dmitry A","family":"Knorre","sequence":"additional","affiliation":[{"name":"Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University , Moscow , Russia"},{"name":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,29]]},"reference":[{"key":"2023122915092599600_evad219-B1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.gene.2016.08.050","article-title":"Syllidae mitochondrial gene order is unusually variable for 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