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The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan\u2010genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome <jats:italic>Brachypodium distachyon<\/jats:italic> and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable \u201coccupancy\u201d in the pan\u2010genome \u2013 genes which are either present in all studied genotypes or missing in some genotypes \u2013 show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought\u2010stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan\u2010genes are under\u2010represented among several modules, while other modules are over\u2010enriched for low\u2010occupancy pan\u2010genes. We also provide new insight into the regulation of drought response in <jats:italic>B.\u00a0distachyon<\/jats:italic>, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan\u2010genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.<\/jats:p>","DOI":"10.1111\/mec.16661","type":"journal-article","created":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T14:39:38Z","timestamp":1660747178000},"page":"5285-5306","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Patterns of pan\u2010genome occupancy and gene coexpression under water\u2010deficit in <i>Brachypodium distachyon<\/i>"],"prefix":"10.1111","volume":"31","author":[{"given":"Rub\u00e9n","family":"Sancho","sequence":"first","affiliation":[{"name":"Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca University of Zaragoza  Huesca Spain"},{"name":"Unidad Associada al CSIC, Grupo de Bioqu\u00edmica Grupo de Bioqu\u00edmica, Biof\u00edsica y Biolog\u00eda Computacional (BIFI, UNIZAR)  Zaragoza Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pilar","family":"Catal\u00e1n","sequence":"additional","affiliation":[{"name":"Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca University of Zaragoza  Huesca Spain"},{"name":"Unidad Associada al CSIC, Grupo de Bioqu\u00edmica Grupo de Bioqu\u00edmica, Biof\u00edsica y Biolog\u00eda Computacional (BIFI, UNIZAR)  Zaragoza Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5462-907X","authenticated-orcid":false,"given":"Bruno","family":"Contreras\u2010Moreira","sequence":"additional","affiliation":[{"name":"Unidad Associada al CSIC, Grupo de Bioqu\u00edmica Grupo de Bioqu\u00edmica, Biof\u00edsica y Biolog\u00eda Computacional (BIFI, UNIZAR)  Zaragoza Spain"},{"name":"Estaci\u00f3n Experimental de Aula Dei\u2010Consejo Superior de Investigaciones Cient\u00edficas  Zaragoza Spain"},{"name":"Fundaci\u00f3n ARAID  Zaragoza Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas E.","family":"Juenger","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology The University of Texas at Austin  Austin Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6772-6987","authenticated-orcid":false,"given":"David L.","family":"Des Marais","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering Massachusetts Institute of Technology  Cambridge Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,8,26]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/35019019"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.05.021"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/pcp\/pcm013"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/pcp\/pcv165"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477\u2010020\u20100733\u20100"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ert185"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1161\/circgen.117.001946"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/mp\/sss160"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.2307\/3870060"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep42131"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u20107\u201040"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2014.05.002"},{"key":"e_1_2_10_16_1","first-page":"9","volume-title":"Genetics and genomics of Brachypodium. 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