{"entity": "researcher", "timestamp": "2026-08-22T07:48:10.040Z", "family": "Simakov", "given": "Oleg", "initials": "O", "orcid": "0000-0002-3585-4511", "affiliations": ["Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5377c9c4c71468c8e60ac2dfe56ee94.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5377c9c4c71468c8e60ac2dfe56ee94"}}, "publications": [{"entity": "publication", "iuid": "bc9d19e9abb546cfb2de415c68ba7546", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc9d19e9abb546cfb2de415c68ba7546.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc9d19e9abb546cfb2de415c68ba7546"}}, "title": "A genome resource for the marine annelid Platynereis spp.", "authors": [{"family": "Mutemi", "given": "Kevin Nzumbi", "initials": "KN", "orcid": "0000-0002-6426-2363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96cb858ec634402ab61f2c8a2963c65c.json"}}, {"family": "Simakov", "given": "Oleg", "initials": "O", "orcid": "0000-0002-3585-4511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5377c9c4c71468c8e60ac2dfe56ee94.json"}}, {"family": "Pan", "given": "Leslie", "initials": "L", "orcid": "0000-0002-2408-4259", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9fcbc9ba63a483f947caf2c873137da.json"}}, {"family": "Santangeli", "given": "Luca", "initials": "L", "orcid": "0000-0001-9600-6164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/886738b7a2d942f28b6febdec005ceaf.json"}}, {"family": "Null", "given": "Ryan Wesley", "initials": "RW", "orcid": "0000-0002-3830-4152", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cd0ad321bdc4192bb5afac9902314f1.json"}}, {"family": "Handberg-Thorsager", "given": "Mette", "initials": "M", "orcid": "0000-0002-3908-7233", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27e5a45c3529449eb63db9b6e5168838.json"}}, {"family": "Vellutini", "given": "Bruno Cossermelli", "initials": "BC", "orcid": "0000-0002-0000-9465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4071ec4a3d284ad5984323c88432bded.json"}}, {"family": "Peterson", "given": "Kevin J", "initials": "KJ", "orcid": "0000-0002-6780-0964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13b1b005ccf0443e8f4441890ae833d0.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "Savage", "given": "Emily", "initials": "E", "orcid": "0000-0003-3391-7571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4863e2e90204f9b999fe8103834aa70.json"}}, {"family": "Lopez", "given": "Mireia Osuna", "initials": "MO", "orcid": "0000-0001-7724-444X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82fd8b97a25c43a0a976da54ca9005a7.json"}}, {"family": "Hercog", "given": "Rajna", "initials": "R"}, {"family": "Provaznik", "given": "Jan", "initials": "J"}, {"family": "Ordo\u00f1ez-Rueda", "given": "Diana", "initials": "D"}, {"family": "Azevedo", "given": "Nayara", "initials": "N"}, {"family": "Gazave", "given": "Eve", "initials": "E", "orcid": "0000-0002-4647-6640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa2145abe5f44641aa2c0295bd5b4ba7.json"}}, {"family": "Vervoort", "given": "Michel", "initials": "M", "orcid": "0000-0002-5995-2140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fed9ac1fcb5d4ab0a291f80c10bf0717.json"}}, {"family": "Tomancak", "given": "Pavel", "initials": "P", "orcid": "0000-0002-2222-9370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9498f9b902d455ca5d1a4346a32e2c8.json"}}, {"family": "Tan", "given": "Wenhua", "initials": "W"}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1f0e31e9346484b8709096822e47d19.json"}}, {"family": "Benes", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-0352-2547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1bf0a09799e4e338ecc55f4712e70b4.json"}}, {"family": "Hui", "given": "Jerome", "initials": "J", "orcid": "0000-0003-1355-8495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e007a542ac745b3806f32717a1c7db3.json"}}, {"family": "Helm", "given": "Conrad", "initials": "C", "orcid": "0000-0002-0308-8402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/272a9436329f4946a9e988543448b8e3.json"}}, {"family": "\u00d6zpolat", "given": "B Duygu", "initials": "BD", "orcid": "0000-0002-1900-965X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/077b6d9102bf4bbf933a27ec1bd2b40e.json"}}, {"family": "Arendt", "given": "Detlev", "initials": "D", "orcid": "0000-0001-7833-050X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bfd7c6c45f7406dba72d3fd5a5f17e8.json"}}], "type": "journal article", "published": "2025-07-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "665", "issn-l": "1471-2164"}, "abstract": "The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~ 1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation (~ 3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.", "doi": "10.1186/s12864-025-11727-2", "pmid": "40660120", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12257675"}, {"db": "pii", "key": "10.1186/s12864-025-11727-2"}], "notes": [], "created": "2026-08-21T12:38:12.076Z", "modified": "2026-08-21T12:38:12.885Z"}, {"entity": "publication", "iuid": "8e542164d999440fb587556e82197d93", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8e542164d999440fb587556e82197d93.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8e542164d999440fb587556e82197d93"}}, "title": "The genomes of all lungfish inform on genome expansion and tetrapod evolution.", "authors": [{"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30e964cee3c44ef3af50e3ea526dc085.json"}}, {"family": "Woltering", "given": "Joost M", "initials": "JM", "orcid": "0000-0002-2630-6572", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc1a407da55241fd8c553c6092e4b6df.json"}}, {"family": "Irisarri", "given": "Iker", "initials": "I", "orcid": "0000-0002-3628-1137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d079957cb2214eb3a334548d6f60a259.json"}}, {"family": "Du", "given": "Kang", "initials": "K", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e9537e7e0c140afb29496bfbf6de5f5.json"}}, {"family": "Kneitz", "given": "Susanne", "initials": "S"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Brown", "given": "Thomas", "initials": "T", "orcid": "0000-0001-8293-4816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d5b348d6b2a4e6b94624f45b18757ab.json"}}, {"family": "Franchini", "given": "Paolo", "initials": "P", "orcid": "0000-0002-8184-1463", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99050c21a7aa483b89907e4369d75020.json"}}, {"family": "Li", "given": "Jing", "initials": "J", "orcid": "0000-0002-0174-3370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/051eb693e82d4e8db8b41de36384e26f.json"}}, {"family": "Li", "given": "Ming", "initials": "M", "orcid": "0000-0001-7049-8666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac3f50a34fe444a1ab21757164a62b70.json"}}, {"family": "Adolfi", "given": "Mateus", "initials": "M"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "de Freitas Sousa", "given": "Josane", "initials": "J"}, {"family": "Chen", "given": "Zhuoxin", "initials": "Z"}, {"family": "Jacinto", "given": "Sandra", "initials": "S"}, {"family": "Kvon", "given": "Evgeny Z", "initials": "EZ", "orcid": "0000-0002-1562-0945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b29e1bbebb404ff8a4f952d55e0fb4fb.json"}}, {"family": "Correa de Oliveira", "given": "Luis Rog\u00e9rio", "initials": "LR"}, {"family": "Monteiro", "given": "Erika", "initials": "E"}, {"family": "Baia Amaral", "given": "Danielson", "initials": "D"}, {"family": "Burmester", "given": "Thorsten", "initials": "T", "orcid": "0000-0002-5772-7863", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a984479edc68463297ae66ea257060c7.json"}}, {"family": "Chalopin", "given": "Domitille", "initials": "D"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Myers", "given": "Eugene", "initials": "E", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf74ba4bae3546eca812b29793341604.json"}}, {"family": "Simakov", "given": "Oleg", "initials": "O", "orcid": "0000-0002-3585-4511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5377c9c4c71468c8e60ac2dfe56ee94.json"}}, {"family": "Schneider", "given": "Igor", "initials": "I", "orcid": "0000-0002-9046-7338", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40fa9b88eab241cdb06869b18dd139d1.json"}}, {"family": "Meyer", "given": "Axel", "initials": "A", "orcid": "0000-0002-0888-8193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92fca58ac7524258856e187411db17b3.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "634", "issue": "8032", "pages": "96-103", "issn-l": "0028-0836"}, "abstract": "The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Kr\u00fcppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.", "doi": "10.1038/s41586-024-07830-1", "pmid": "39143221", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2020022"}, {"db": "pmc", "key": "PMC11514621"}, {"db": "pii", "key": "10.1038/s41586-024-07830-1"}, {"db": "BioProject", "key": "PRJNA808321, PRJNA808322, PRJNA813994, PRJNA813995, PRJNA981572"}], "notes": [], "created": "2026-08-21T11:51:20.665Z", "modified": "2026-08-21T11:51:21.165Z"}]}