{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T13:06:50Z","timestamp":1781701610653,"version":"3.54.5"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,12,19]],"date-time":"2020-12-19T00:00:00Z","timestamp":1608336000000},"content-version":"vor","delay-in-days":79,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"UC Davis New Research Initiatives and Interdisciplinary Research Grant"},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["CA-D-PLS-2511-H"],"award-info":[{"award-number":["CA-D-PLS-2511-H"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390686111"],"award-info":[{"award-number":["390686111"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well-suited model system to study sex determination in plants. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole-genome sequencing of male and female pools from 2 independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex-linked genes. Consequently, we employed an alignment-free k-mer comparison which enabled us to identify a large number of male-specific k-mers. We assembled male-specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex-determination system in the species. We were able to identify the potential Y chromosome in the A. palmeri draft genome sequence as 90% of our male-specific sequence aligned to a single scaffold. Based on our findings, we suggest an intermediate evolutionary state of dioecy with a young Y chromosome in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.<\/jats:p>","DOI":"10.1093\/jhered\/esaa047","type":"journal-article","created":{"date-parts":[[2020,11,16]],"date-time":"2020-11-16T07:17:38Z","timestamp":1605511058000},"page":"606-612","source":"Crossref","is-referenced-by-count":15,"title":["Male Linked Genomic Region Determines Sex in Dioecious\n                    <i>Amaranthus palmeri<\/i>"],"prefix":"10.1093","volume":"111","author":[{"given":"Ca\u0301tia Jose\u0301","family":"Neves","sequence":"first","affiliation":[{"name":"Institute for Plant Sciences, University of Cologne , Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maor","family":"Matzrafi","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of California, Davis , Davis, CA"},{"name":"Department of Plant Pathology and Weed Research, Agricultural Research Organization, Newe Ya\u2019ar Research Center , Ramat Yishai, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meik","family":"Thiele","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences, University of Cologne , Cologne, Germany"},{"name":"Cluster of Excellence on Plant Sciences, University of Cologne , Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Lorant","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of California, Davis , Davis, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohsen B","family":"Mesgaran","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of California, Davis , Davis, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7136-0589","authenticated-orcid":false,"given":"Markus G","family":"Stetter","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences, University of Cologne , Cologne, Germany"},{"name":"Cluster of Excellence on Plant Sciences, University of Cologne , Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,19]]},"reference":[{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/oxfordjournals.aob.a083792","article-title":"Cytological studies in the cycads: sex chromosomes in cycas","volume":"26","author":"Abraham","year":"1962","journal-title":"Ann Bot (Lond)"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1126\/science.1257225","article-title":"A y-chromosome\u2013encoded small RNA acts as a sex determinant in persimmons","volume":"346","author":"Akagi","year":"2014","journal-title":"Science"},{"key":"2023030918444009300_","first-page":"102","article-title":"Amaranthus spinosus-a review","volume":"5","author":"Asha","year":"2016","journal-title":"Bull. Environ. Pharmacol. 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Sci"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1086\/283342","article-title":"A model for the evolution of dioecy and gynodioecy","volume":"112","author":"Charlesworth","year":"1978","journal-title":"Am Naturalist"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1146\/annurev-arplant-043015-111911","article-title":"Plant sex chromosomes","volume":"67","author":"Charlesworth","year":"2016","journal-title":"Annu Rev Plant Biol"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/jxb\/ers322","article-title":"Plant sex chromosome 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Biology and Evolution"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1017\/wsc.2019.27","article-title":"Sex-specific markers for waterhemp (Amaranthus tuberculatus) and palmer amaranth (Amaranthus palmeri)","volume":"67","author":"Montgomery","year":"2019","journal-title":"Weed Sci"},{"key":"2023030918444009300_","first-page":"275","article-title":"New infrageneric taxa and combinations in Amaranthus (Amaranthaceae)","volume":"33","author":"Mosyakin","year":"1996","journal-title":"Ann Bot Fenn"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/hdy.2014.125","article-title":"Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.)","volume":"114","author":"Pucholt","year":"2015","journal-title":"Heredity (Edinb)"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.3732\/ajb.1400196","article-title":"The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database","volume":"101","author":"Renner","year":"2014","journal-title":"Am J Bot"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1614\/WT-D-12-00167.1","article-title":"Assessment of weed management practices and problem weeds in the midsouth united states\u2014soybean: a consultant\u2019s perspective","volume":"27","author":"Riar","year":"2013","journal-title":"Weed Technol"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1017\/S0043174500091815","article-title":"Full-season palmer amaranth (Amaranthus palmeri) interference with cotton (Gossypium hirsutum).","volume":"47","author":"Rowland","year":"1999","journal-title":"Weed Sci"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1508\/cytologia.63.459","article-title":"Characterization; genome sizes and 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2008\/2009","volume":"60","author":"Webster","year":"2012","journal-title":"Weed Sci"},{"key":"2023030918444009300_","first-page":"217","article-title":"The mechanism of sex determination in dioecious flowering plants","volume-title":"Advances in genetics","author":"Westergaard","year":"1958"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1002\/j.1537-2197.1988.tb14191.x","article-title":"Intraspecific variation in germination requirements and growth in Amaranthus dubius","volume":"75","author":"Wulff","year":"1988","journal-title":"Am J Bot"},{"key":"2023030918444009300_","doi-asserted-by":"crossref","first-page":"1246338","DOI":"10.1126\/science.1246338","article-title":"Complex evolutionary trajectories of sex chromosomes across bird taxa","volume":"346","author":"Zhou","year":"2014","journal-title":"Science"}],"container-title":["Journal of 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