{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T13:36:40Z","timestamp":1791725800555,"version":"4.3.4"},"reference-count":31,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    The\n                    <jats:italic>CIPK<\/jats:italic>\n                    (CBL-interacting protein kinase) gene family serves as a crucial component of calcium-mediated signaling pathways in plants, playing vital roles in abiotic stress responses and developmental regulation. Despite their functional importance, systematic comparative analyses of\n                    <jats:italic>CIPK<\/jats:italic>\n                    gene families between cereal species with distinct physiological adaptations remain limited. To address this knowledge gap, we present a comprehensive comparative genomic analysis of\n                    <jats:italic>CIPK<\/jats:italic>\n                    gene families in two ecologically and physiologically divergent cereal crops - rice (\n                    <jats:italic>Oryza sativa<\/jats:italic>\n                    , a C\n                    <jats:sub>3<\/jats:sub>\n                    species adapted to aquatic environments) and foxtail millet (\n                    <jats:italic>Setaria italica<\/jats:italic>\n                    , a C\n                    <jats:sub>4<\/jats:sub>\n                    species with superior drought tolerance). We identified 33 and 35\n                    <jats:italic>CIPK<\/jats:italic>\n                    genes in rice and foxtail millet, respectively, revealing conserved synteny but distinct evolutionary trajectories. Chromosomal mapping showed uneven distributions of\n                    <jats:italic>CIPK<\/jats:italic>\n                    genes in both species. Segmental duplications may have significantly contributed to family expansion (20\/33 genes in rice; 19\/35 in foxtail millet). Phylogenetic analysis classified members into six clades in foxtail millet and rice. Structural analysis revealed clade-specific exon-intron patterns, with complex architectures (12\u201320 exons) in Clade I versus simplified structures (1\u20133 exons) in other clades. Comparative genomics identified 26 orthologous pairs, though some genes (e.g.,\n                    <jats:italic>OsCIPK27<\/jats:italic>\n                    ) lacked detectable orthologs, indicating species-specific gene loss. Notably, foxtail millet CIPK exhibited lower instability indices, which may indicate potential stability differences. In addition, foxtail millet showed complete conservation of calcium-sensing NAF domains, whereas rice showed one NAF-deficient member (OsCIPK4). Promoter analysis identified species-specific\n                    <jats:italic>cis<\/jats:italic>\n                    -element enrichment: rice\n                    <jats:italic>CIPK<\/jats:italic>\n                    were enriched in drought\/ABA-responsive elements, whereas foxtail millet showed greater light-responsive motif diversity. Expression profiling revealed tissue-specific patterns, with foxtail millet displaying more leaf-preferential expression (10 genes vs. 7 in rice), potentially linked to C\n                    <jats:sub>4<\/jats:sub>\n                    photosynthesis. Under abiotic stress conditions, rice\n                    <jats:italic>CIPK<\/jats:italic>\n                    genes exhibited strong responses to both salt and cold stressors, whereas foxtail millet\n                    <jats:italic>CIPK<\/jats:italic>\n                    showed greater responsiveness to drought, mirroring their ecological adaptations. These findings provide novel insight into the potential function and evolutionary diversification of calcium signaling components (\n                    <jats:italic>CIPK<\/jats:italic>\n                    ) in C\n                    <jats:sub>3<\/jats:sub>\n                    and C\n                    <jats:sub>4<\/jats:sub>\n                    cereals. They also provide important potential targets for improving the stress resistance of cereal crops.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2025.1710663","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T05:30:44Z","timestamp":1767591044000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Comparative genomics and expression analysis of the CIPK gene family in rice (Oryza sativa) and foxtail millet (Setaria italica)"],"prefix":"10.3389","volume":"16","author":[{"given":"Zhao","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Run","family":"Qian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengpu","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziwei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pingmei","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1283555","article-title":"Genome-wide dissection of AT-hook motif nuclear-localized gene family and their expression profiling for drought and salt stress in rice (Oryza sativa)","volume":"14","author":"Ambadas","year":"2023","journal-title":"Front. 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