{"entity": "researcher", "timestamp": "2026-08-17T01:01:44.055Z", "family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "affiliations": ["Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a"}}, "publications": [{"entity": "publication", "iuid": "3f18e5c79db74984ba3dfc82d76eecf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3"}}, "title": "A pangenome and pantranscriptome of hexaploid oat.", "authors": [{"family": "Avni", "given": "Raz", "initials": "R", "orcid": "0000-0002-0801-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e818aced4e14e529c60a7dd5d396de0.json"}}, {"family": "Kamal", "given": "Nadia", "initials": "N", "orcid": "0000-0002-3258-4130", "researcher": {"href": "https://publications.scilifelab.se/researcher/da83072939d347778c03424c656d1bae.json"}}, {"family": "Bitz", "given": "Lidija", "initials": "L"}, {"family": "Jellen", "given": "Eric N", "initials": "EN", "orcid": "0000-0002-7906-4845", "researcher": {"href": "https://publications.scilifelab.se/researcher/83594761835445f9a5c92cad770ca372.json"}}, {"family": "Bekele", "given": "Wubishet A", "initials": "WA", "orcid": "0000-0002-6463-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea58d9ecc7a45c58a19fd0a36bed3ff.json"}}, {"family": "Angessa", "given": "Tefera T", "initials": "TT"}, {"family": "Auvinen", "given": "Petri", "initials": "P", "orcid": "0000-0002-3947-4778", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b998007ca8b412c8dac49230d5cea94.json"}}, {"family": "Bitz", "given": "Oliver", "initials": "O"}, {"family": "Boyle", "given": "Brian", "initials": "B", "orcid": "0000-0002-0158-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/de076e7c690542cfbc5b2da120521e29.json"}}, {"family": "Canales", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0001-7911-856X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd058ce520fc48de81a2c4f2762659b4.json"}}, {"family": "Carlson", "given": "Craig H", "initials": "CH", "orcid": "0000-0003-2050-5455", "researcher": {"href": "https://publications.scilifelab.se/researcher/f856003d4ec44935812545685e22fe41.json"}}, {"family": "Chapman", "given": "Brett", "initials": "B", "orcid": "0000-0003-4484-2253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4410e6ff3a7d489e84b05dc81edf53ce.json"}}, {"family": "Chawla", "given": "Harmeet Singh", "initials": "HS"}, {"family": "Chen", "given": "Yutang", "initials": "Y", "orcid": "0000-0001-8128-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d3e1845423c4e0389ee86c0986a294d.json"}}, {"family": "Copetti", "given": "Dario", "initials": "D"}, {"family": "Correia de Lemos", "given": "Samara", "initials": "S", "orcid": "0000-0003-3484-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/4105d0322d0c478e8c3758d2d353c3e2.json"}}, {"family": "Dang", "given": "Viet", "initials": "V", "orcid": "0000-0001-6408-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc432298db04432b1285e4530d566de.json"}}, {"family": "Eichten", "given": "Steven R", "initials": "SR", "orcid": "0000-0003-2268-395X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c014d8bcd56b4240a3b8ed3219fac6f2.json"}}, {"family": "Klos", "given": "Kathy Esvelt", "initials": "KE"}, {"family": "Fenn", "given": "Amit M", "initials": "AM", "orcid": "0000-0003-2203-3922", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27d342e880f4692bc1224c520b78dae.json"}}, {"family": "Fiebig", "given": "Anne", "initials": "A", "orcid": "0000-0003-3159-3593", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af17bbf24b34f20a9f433583ff00c05.json"}}, {"family": "Fu", "given": "Yong-Bi", "initials": "YB", "orcid": "0000-0003-3106-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f089f51863447cf88cdb4ec23e009bc.json"}}, {"family": "Gundlach", "given": "Heidrun", "initials": "H", "orcid": "0000-0002-6757-0943", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6d69126dd4a9a9a99827c672b5fa5.json"}}, {"family": "Gupta", "given": "Rajeev", "initials": "R", "orcid": "0000-0002-1451-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd2a62988238458e9ab17d4d7f60f2bb.json"}}, {"family": "Haberer", "given": "Georg", "initials": "G", "orcid": "0000-0002-6612-6939", "researcher": {"href": "https://publications.scilifelab.se/researcher/5313eb519bd24ee3b92a090746ad93a3.json"}}, {"family": "He", "given": "Tianhua", "initials": "T"}, {"family": "Herrmann", "given": "Matthias H", "initials": "MH", "orcid": "0000-0003-1760-6167", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1be02f0c5024c29aa810cb1dcc63c3f.json"}}, {"family": "Himmelbach", "given": "Axel", "initials": "A", "orcid": "0000-0001-7338-0946", "researcher": {"href": "https://publications.scilifelab.se/researcher/473928fe106248bdba303b0455faa930.json"}}, {"family": "Howarth", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0001-9364-0880", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec8235c6e6348d3a4e1f84f0759348b.json"}}, {"family": "Hu", "given": "Haifei", "initials": "H", "orcid": "0000-0003-1070-213X", "researcher": {"href": "https://publications.scilifelab.se/researcher/573e418a00344b0192db99e0c8a4707a.json"}}, {"family": "Isidro Y S\u00e1nchez", "given": "Julio", "initials": "J", "orcid": "0000-0002-9044-3221", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef581d9a44994c798decadb0531b313c.json"}}, {"family": "Itaya", "given": "Asuka", "initials": "A", "orcid": "0000-0003-4132-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfab79c8f493415e9d86932559a40663.json"}}, {"family": "Jannink", "given": "Jean-Luc", "initials": "JL", "orcid": "0000-0003-4849-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df52f0eac0e4649adf4b87e2a702abe.json"}}, {"family": "Jia", "given": "Yong", "initials": "Y", "orcid": "0000-0002-0394-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/078c829a8fc2442da58be531b08381ee.json"}}, {"family": "Kaur", "given": "Rajvinder", "initials": "R"}, {"family": "Knauft", "given": "Manuela", "initials": "M"}, {"family": "Langdon", "given": "Tim", "initials": "T"}, {"family": "Lux", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5543-1911", "researcher": {"href": "https://publications.scilifelab.se/researcher/076281817e274a45819ff2f53f9047cf.json"}}, {"family": "Marmon", "given": "Sofia", "initials": "S", "orcid": "0000-0001-6929-7859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0105355f5c26423f98f7e4429318bb2c.json"}}, {"family": "Marosi", "given": "Vanda", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX", "orcid": "0000-0001-6484-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd32d600030146e9891b324e80708362.json"}}, {"family": "Michel", "given": "Steve", "initials": "S"}, {"family": "Nandety", "given": "Raja Sekhar", "initials": "RS", "orcid": "0000-0002-1129-0790", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6834d990f14f578a96a7b57e06dbf8.json"}}, {"family": "Nilsen", "given": "Kirby T", "initials": "KT"}, {"family": "Paczos-Grz\u0119da", "given": "Edyta", "initials": "E", "orcid": "0000-0001-6273-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a271331d534543a3907db410616d4b.json"}}, {"family": "Pasha", "given": "Asher", "initials": "A", "orcid": "0000-0002-9315-0520", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea77d66f7a040f680e391da2b46ce24.json"}}, {"family": "Prats", "given": "Elena", "initials": "E"}, {"family": "Provart", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0001-5551-7232", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c3f4e8ce0c44e3a74c8c0ad1aa7554.json"}}, {"family": "Ravagnani", "given": "Adriana", "initials": "A"}, {"family": "Reid", "given": "Robert W", "initials": "RW"}, {"family": "Schlueter", "given": "Jessica A", "initials": "JA"}, {"family": "Schulman", "given": "Alan H", "initials": "AH"}, {"family": "Sen", "given": "Taner Z", "initials": "TZ"}, {"family": "Singh", "given": "Jaswinder", "initials": "J", "orcid": "0000-0002-1139-9251", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e830c055e2542d6a2e6388ec3cad25c.json"}}, {"family": "Singh", "given": "Mehtab", "initials": "M", "orcid": "0000-0003-4550-9858", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2c9ff04964e42f08b8e906b51bf0b0d.json"}}, {"family": "Sirijovski", "given": "Nick", "initials": "N", "orcid": "0000-0002-6191-3845", "researcher": {"href": "https://publications.scilifelab.se/researcher/040fc49df77d4171bf2695ae420f2302.json"}}, {"family": "Stein", "given": "Nils", "initials": "N", "orcid": "0000-0003-3011-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ef5173e1214a9f920bcadad30afc70.json"}}, {"family": "Studer", "given": "Bruno", "initials": "B"}, {"family": "Viitala", "given": "Sirja", "initials": "S"}, {"family": "Vronces", "given": "Shauna", "initials": "S"}, {"family": "Walkowiak", "given": "Sean", "initials": "S", "orcid": "0000-0002-3866-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acd3a3bf11144baa35b773b921e23c9.json"}}, {"family": "Wang", "given": "Penghao", "initials": "P", "orcid": "0000-0002-3751-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd3893272754899abcdb06dabaf195e.json"}}, {"family": "Waters", "given": "Amanda J", "initials": "AJ"}, {"family": "Wight", "given": "Charlene P", "initials": "CP", "orcid": "0000-0003-1410-5631", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bffc6376bf8453da9d6ac3b962805b6.json"}}, {"family": "Yan", "given": "Weikai", "initials": "W"}, {"family": "Yao", "given": "Eric", "initials": "E"}, {"family": "Zhang", "given": "Xiao-Qi", "initials": "XQ"}, {"family": "Zhou", "given": "Gaofeng", "initials": "G"}, {"family": "Zhou", "given": "Zhou", "initials": "Z"}, {"family": "Tinker", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0002-2452-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef54eb854d47488f88ffc97360bfef59.json"}}, {"family": "Fiedler", "given": "Jason D", "initials": "JD", "orcid": "0000-0001-7736-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e65e63fd07a4543a61a30ea653254d7.json"}}, {"family": "Li", "given": "Chengdao", "initials": "C", "orcid": "0000-0002-9653-2700", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3e4736c749c4b07b76e1ae98c4c9bbe.json"}}, {"family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}}, {"family": "Spannagl", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0701-7035", "researcher": {"href": "https://publications.scilifelab.se/researcher/88a57f18a3794d1aaf7af7c579697860.json"}}, {"family": "Mascher", "given": "Martin", "initials": "M", "orcid": "0000-0001-6373-6013", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2d033b05734d53a888db3e03edee0a.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836"}, "abstract": "Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.", "doi": "10.1038/s41586-025-09676-7", "pmid": "41162711", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09676-7"}], "notes": [], "created": "2025-11-19T07:39:59.482Z", "modified": "2025-11-28T10:46:37.749Z"}, {"entity": "publication", "iuid": "c0bb50ac623641d88b32b975f7e3b455", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0bb50ac623641d88b32b975f7e3b455.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0bb50ac623641d88b32b975f7e3b455"}}, "title": "The mosaic oat genome gives insights into a uniquely healthy cereal crop.", "authors": [{"family": "Kamal", "given": "Nadia", "initials": "N"}, {"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N", "orcid": "0000-0001-7216-5320", "researcher": {"href": "https://publications.scilifelab.se/researcher/117e1cc25e4545298e212d86b3ee8ce3.json"}}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Gundlach", "given": "Heidrun", "initials": "H", "orcid": "0000-0002-6757-0943", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6d69126dd4a9a9a99827c672b5fa5.json"}}, {"family": "Haberer", "given": "Georg", "initials": "G", "orcid": "0000-0002-6612-6939", "researcher": {"href": "https://publications.scilifelab.se/researcher/5313eb519bd24ee3b92a090746ad93a3.json"}}, {"family": "Juh\u00e1sz", "given": "Ang\u00e9la", "initials": "A"}, {"family": "Lux", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5543-1911", "researcher": {"href": "https://publications.scilifelab.se/researcher/076281817e274a45819ff2f53f9047cf.json"}}, {"family": "Bose", "given": "Utpal", "initials": "U"}, {"family": "Tye-Din", "given": "Jason A", "initials": "JA", "orcid": "0000-0001-7687-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dacb233f9d747f7802937fdbfa63d07.json"}}, {"family": "Lang", "given": "Daniel", "initials": "D", "orcid": "0000-0002-2166-0716", "researcher": {"href": "https://publications.scilifelab.se/researcher/a42c82d2c3944382811323db528b074f.json"}}, {"family": "van Gessel", "given": "Nico", "initials": "N", "orcid": "0000-0002-0606-246X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f634bf44243b4c9e8862d2fcbb637357.json"}}, {"family": "Reski", "given": "Ralf", "initials": "R", "orcid": "0000-0002-5496-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f01ef88d61741e8a2fa6ad36d545f52.json"}}, {"family": "Fu", "given": "Yong-Bi", "initials": "YB"}, {"family": "Sp\u00e9gel", "given": "Peter", "initials": "P", "orcid": "0000-0002-6092-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e06a5bbd6114a248eafb168782d0b27.json"}}, {"family": "Ceplitis", "given": "Alf", "initials": "A"}, {"family": "Himmelbach", "given": "Axel", "initials": "A"}, {"family": "Waters", "given": "Amanda J", "initials": "AJ"}, {"family": "Bekele", "given": "Wubishet A", "initials": "WA"}, {"family": "Colgrave", "given": "Michelle L", "initials": "ML"}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}, {"family": "Stein", "given": "Nils", "initials": "N", "orcid": "0000-0003-3011-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ef5173e1214a9f920bcadad30afc70.json"}}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX", "orcid": "0000-0001-6484-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd32d600030146e9891b324e80708362.json"}}, {"family": "Jellen", "given": "Eric N", "initials": "EN", "orcid": "0000-0002-7906-4845", "researcher": {"href": "https://publications.scilifelab.se/researcher/83594761835445f9a5c92cad770ca372.json"}}, {"family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}}, {"family": "Tinker", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0002-2452-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef54eb854d47488f88ffc97360bfef59.json"}}, {"family": "Mascher", "given": "Martin", "initials": "M", "orcid": "0000-0001-6373-6013", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2d033b05734d53a888db3e03edee0a.json"}}, {"family": "Olsson", "given": "Olof", "initials": "O"}, {"family": "Spannagl", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0701-7035", "researcher": {"href": "https://publications.scilifelab.se/researcher/88a57f18a3794d1aaf7af7c579697860.json"}}, {"family": "Sirijovski", "given": "Nick", "initials": "N", "orcid": "0000-0002-6191-3845", "researcher": {"href": "https://publications.scilifelab.se/researcher/040fc49df77d4171bf2695ae420f2302.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "606", "issue": "7912", "pages": "113-119"}, "abstract": "Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.", "doi": "10.1038/s41586-022-04732-y", "pmid": "35585233", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9159951"}, {"db": "pii", "key": "10.1038/s41586-022-04732-y"}], "notes": [], "created": "2022-08-19T08:37:48.764Z", "modified": "2024-01-16T13:48:36.250Z"}]}