{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T06:31:40Z","timestamp":1786516300711,"version":"build-2736575974"},"reference-count":67,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009110","name":"Natural Science Foundation of Xinjiang Uygur Autonomous Region","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009110","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Cotton (\n                    <jats:italic>Gossypium<\/jats:italic>\n                    spp.) is highly susceptible to abiotic stresses, including temperature extremes, drought, and salinity. The diploid species\n                    <jats:italic>Gossypium arboreum<\/jats:italic>\n                    retains stress adaptive traits that are poorly represented in modern tetraploid cultivars, yet the evolutionary and regulatory bases of these ploidy associated differences remain insufficiently understood. Here, we performed a comparative transcriptomic analysis of 54 seedling leaf RNA-seq libraries from\n                    <jats:italic>Gossypium arboreum<\/jats:italic>\n                    ,\n                    <jats:italic>Gossypium hirsutum<\/jats:italic>\n                    , and\n                    <jats:italic>Gossypium barbadense<\/jats:italic>\n                    subjected to four abiotic stress treatments. By integrating standardized cross-species normalization with an optimized gene co-expression network framework, we minimized interspecific technical heterogeneity and enabled robust comparison of stress responsive regulatory architectures. Consensus network analysis revealed marked topological divergence between diploid and tetraploid cotton. The\n                    <jats:italic>G. arboreum<\/jats:italic>\n                    A\n                    <jats:sub>2<\/jats:sub>\n                    network showed strong structural conservation with the A\n                    <jats:sub>t<\/jats:sub>\n                    subgenome of\n                    <jats:italic>G. hirsutum<\/jats:italic>\n                    , whereas extensive co-expression rewiring was detected in the A\n                    <jats:sub>t<\/jats:sub>\n                    subgenome of\n                    <jats:italic>G. barbadense<\/jats:italic>\n                    , which may reflect lineage-specific regulatory remodeling of stress-response programs after allopolyploidization. By integrating conserved multi-species networks with five genome or subgenome specific networks, we identified 54 core cold-repressed candidate genes, including a BBR-BPC transcription factor potentially associated with ethylene related stress signaling. The divergent topology of the cold-responsive subnetwork defined by these candidates suggests extensive transcriptional reprogramming associated with polyploid evolution. Module preservation analysis also uncovered an A\n                    <jats:sub>2<\/jats:sub>\n                    -specific heat-responsive module centered on an ERF transcription factor. In a distinct drought\/heat co-responsive module, another ERF was predicted to coordinate both a heat shock factor (HSF) and an ABA responsive TALE transcription factor, suggesting potential regulatory crosstalk between heat and drought signaling pathways. Collectively, our study resolves conserved and lineage-specific components of cotton abiotic stress regulation and provides candidate regulators for resilience oriented molecular breeding.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1889274","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T05:59:30Z","timestamp":1786514370000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Conservation and divergence of abiotic stress-responsive gene co-expression networks in diploid and tetraploid cotton"],"prefix":"10.3389","volume":"17","author":[{"given":"Heng","family":"Wang","sequence":"first","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumeng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Zhao","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueying","family":"Guan","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junduo","family":"Wang","sequence":"additional","affiliation":[{"name":"Xinjiang Key Laboratory of Cotton Genetic Improvement and Intelligent Production\/Xinjiang Cotton Technology Innovation Center, Cotton Research Institute of Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region (National Cotton Engineering Technology Research Center)","place":["Urumuqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luyao","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]},{"name":"Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences \/ Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs \/ Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province","place":["Haikou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/s12870-017-1078-3","article-title":"GaMYB85, an R2R3 MYB gene, in transgenic Arabidopsis plays an important role in drought tolerance","volume":"17","author":"Butt","year":"2017","journal-title":"BMC Plant Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1007\/s11103-021-01169-1","article-title":"The lincRNA XH123 is involved in cotton cold-stress regulation","volume":"106","author":"Cao","year":"2021","journal-title":"Plant Mol. 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