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However, the genetic interaction between the recipient genome(s) and the alien chromosomes remains largely unclear. Here, we analyzed the genomic composition and gene expression of 2 purple-leaved Brassica napus alien addition lines carrying chromosome B05 from B. juncea: the monosomic line ZYCB3 (MAAL, 2n = 39, AACC + 1B05) and the disomic line ZY52 (DAAL, 2n = 40, AACC + 2B05). We assembled a chromosome-level genome of the DAAL ZY52 disomic line and characterized its genomic variation and chromosome introgression patterns. In addition to chromosome B05, multiple introgressed fragments derived from the donor B. juncea line ZYJC were identified, revealing extensive genome remodeling during distant hybridization and backcross breeding. We then used multi-omics approaches to explore chromosomal interactions and the regulation of anthocyanin biosynthesis. Notably, the addition of chromosome B05 was associated with stronger repression of homoeologous genes on C-subgenome chromosomes than on A-subgenome chromosomes. In ZY52, homoeologous genes on chromosome C01 showed reduced expression, whereas in the ZYCB3 monosomic line reduced expression was observed on both C01 and C02. Comparative transcriptomic and metabolomic analyses further showed that highly expressed anthocyanin biosynthesis genes (ABGs) on chromosome B05contributed to anthocyanin accumulation and the purple-leaf phenotype in both addition lines. Overall, this study provides new insights into interchromosomal interactions, genome remodeling, and phenotypic variation in alien addition lines.<\/jats:p>","DOI":"10.1093\/plphys\/kiag688","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:04:21Z","timestamp":1789473861000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome assembly and subgenomic interactions in\n                    <i>Brassica napus<\/i>\n                    additional lines with an alien B05 chromosome from\n                    <i>B. juncea<\/i>"],"prefix":"10.1093","volume":"202","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-7972-8763","authenticated-orcid":false,"given":"Yi","family":"Liu","sequence":"first","affiliation":[{"name":"College of Life Sciences, Gannan Normal University , Ganzhou ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8106-2960","authenticated-orcid":false,"given":"Chaomin","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Gannan Normal University , Ganzhou ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1189-695X","authenticated-orcid":false,"given":"Haidong","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Gannan Normal University , Ganzhou ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5807-932X","authenticated-orcid":false,"given":"Shubei","family":"Wan","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Gannan Normal University , Ganzhou ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3950-210X","authenticated-orcid":false,"given":"Xianhong","family":"Ge","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, National Research Center of Rapeseed Engineering and Technology, Huazhong Agricultural University , Wuhan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3510-8906","authenticated-orcid":false,"given":"Qinyong","family":"Yang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, National Research Center of Rapeseed Engineering and Technology, Huazhong Agricultural University , Wuhan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaiyun","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, National Research Center of Rapeseed Engineering and Technology, Huazhong Agricultural University , Wuhan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0318-4194","authenticated-orcid":false,"given":"Martin A","family":"Lysak","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Faculty of Science, Masaryk University , Brno ,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6968-9502","authenticated-orcid":false,"given":"Chen","family":"Tan","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Gannan Normal University , Ganzhou ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Cui","sequence":"additional","affiliation":[{"name":"Crop Research Institute, Sichuan Academy of Agricultural 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