{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T01:50:05Z","timestamp":1791510605598,"version":"4.3.4"},"reference-count":25,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:00:00Z","timestamp":1791417600000},"content-version":"vor","delay-in-days":37,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Physiologia Plantarum"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Navara (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Oryza sativa<\/jats:italic>\n                    <\/jats:styled-content>\n                    L.) is a traditional pigmented rice landrace from Kerala, India, recognized for its nutritional and medicinal importance. However, its genome\u2010wide sequence variation and population\u2010genetic context remain insufficiently characterized. Here, we present a whole\u2010genome sequence resource for a single Navara accession, with particular emphasis on sequence variation in genes associated with anthocyanin and flavonoid biosynthesis. Paired\u2010end whole\u2010genome sequencing generated 58.7 million reads, providing approximately 30\u00d7 genome coverage. Reference\u2010guided analysis using the well\u2010annotated IRGSP\u20101.0 genome identified 4,118,622 high\u2010confidence variants, comprising 3,513,668 SNPs and 604,954 INDELs. Among the 19 selected anthocyanin\u2010 and flavonoid\u2010related genes, 561 SNPs were identified and characterized according to their genomic context and predicted consequences. Comparison with the Rice3K dataset identified 131 variants in these genes that were not observed in the comparison dataset. Genome\u2010wide principal component analysis placed the sequenced Navara accession closest to the Aus\/boro genetic group, while identity\u2010by\u2010state analysis identified Karutha Seenati as the closest accession among those compared using the selected loci. Several variant\u2010containing regions overlapped previously reported rice QTL intervals, providing genomic context for further investigation without implying genetic association or causality. De novo assembly of reference\u2010unmapped reads generated approximately 9.29\u2009Mb of additional sequence, including predicted genes and repetitive elements, while comparison with the PanOryza pangenome indicated that most predicted genes were represented within the broader rice gene pool. Collectively, these datasets provide a reusable genomic resource for comparative genomics, genetic\u2010diversity analysis, marker development, conservation of traditional rice germplasm, and future functional investigation of pigmentation, nutritional, and agronomic traits.\n                  <\/jats:p>","DOI":"10.1111\/ppl.71148","type":"journal-article","created":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T01:02:24Z","timestamp":1791507744000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Whole\u2010Genome Sequence Resource for the Medicinal Rice Landrace Navara"],"prefix":"10.1111","volume":"178","author":[{"given":"Praveena","family":"Murugan","sequence":"first","affiliation":[{"name":"Department of Genomic Science Central University of Kerala  Kasaragod Kerala India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5524-9582","authenticated-orcid":false,"given":"Saumya","family":"Dwivedi","sequence":"additional","affiliation":[{"name":"Department of Genomic Science Central University of Kerala  Kasaragod Kerala India"},{"name":"Department of Computer Science Central University of Kerala  Kasaragod Kerala India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2717-6184","authenticated-orcid":false,"given":"Nikitha","family":"Jayachandran","sequence":"additional","affiliation":[{"name":"Department of Genomic Science Central University of Kerala  Kasaragod Kerala India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2875-2290","authenticated-orcid":false,"given":"Manickavelu","family":"Alagu","sequence":"additional","affiliation":[{"name":"Department of Genomic Science Central University of Kerala  Kasaragod Kerala India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,8]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1039"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodres.2014.03.007"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1155\/2008\/524847"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/1541\u20104337.70355"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2007.05.062"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.12.006"},{"key":"e_1_2_11_8_1","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/978-3-642-83962-7_18","volume-title":"Molecular Techniques in Taxonomy","author":"Doyle J.","year":"1991"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u2010313X.2006.02958.x"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.104.035642"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/1939\u20108433\u20106\u20104"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1005810616885"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jfca.2022.104742"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1360\u20101385(00)01860\u20104"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0900992106"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00438\u2010021\u201001844\u20104"},{"key":"e_1_2_11_17_1","first-page":"83","article-title":"Rice GIs of Kerala: Gap in Desired and Achieved Outcomes","volume":"26","author":"Radhika A. 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