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Ornamental camellias have a diverse range of resources, including different bud variations from <jats:italic>Camellia<\/jats:italic> spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we report the chromosomal-level reference genome of <jats:italic>C. japonica<\/jats:italic> through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F<jats:sub>1<\/jats:sub> hybrids between <jats:italic>C. japonica<\/jats:italic> and <jats:italic>C. chekiangoleosa<\/jats:italic>. We identify two whole-genome duplication events in <jats:italic>C. japonica<\/jats:italic>: one is a shared ancient \u03b3 event, and the other is revealed to be specific to genus <jats:italic>Camellia<\/jats:italic>. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the <jats:italic>AGAMOUS<\/jats:italic> loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of <jats:italic>C. japonica<\/jats:italic> and <jats:italic>C. azalea<\/jats:italic>\u2014a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including <jats:italic>GIGANTEA<\/jats:italic> and <jats:italic>CONSTANS<\/jats:italic> of the photoperiod pathway, have been disrupted in <jats:italic>C. azalea<\/jats:italic>. Furthermore, we reveal that the distinctive expression patterns of <jats:italic>FLOWERING LOCUS T<\/jats:italic> can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in <jats:italic>GIGANTEA<\/jats:italic>, <jats:italic>CONSTANS<\/jats:italic>, and <jats:italic>FLOWERING LOCUS T<\/jats:italic> is central to achieve seasonality.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Through the genomic and comparative genomics characterizations of ornamental <jats:italic>Camellia<\/jats:italic> spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12915-024-01851-y","type":"journal-article","created":{"date-parts":[[2024,2,27]],"date-time":"2024-02-27T13:02:31Z","timestamp":1709038951000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia"],"prefix":"10.1186","volume":"22","author":[{"given":"Zhikang","family":"Hu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhengqi","family":"Fan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sijia","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minyan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingchuan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianjin","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weixin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yupeng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yifan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaxuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingkun","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinlei","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiyuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0720-5311","authenticated-orcid":false,"given":"Hengfu","family":"Yin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,2,27]]},"reference":[{"key":"1851_CR1","volume-title":"A revision of the genus Camellia","author":"JR Sealy","year":"1958","unstructured":"Sealy JR. 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