{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T07:25:34Z","timestamp":1786951534829,"version":"build-2736575974"},"reference-count":85,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"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:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Gene expression in plants is inherently dynamic, shifting rapidly during development and in response to environmental stimuli. However, many essential cellular processes require remarkable transcriptomic stability. The identity, genomic features, and evolutionary conservation of stably expressed genes (SEGs) in plants across broad evolutionary scales remain poorly understood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We analyzed comprehensive transcriptome atlases from five species representing major clades of angiosperms (\n                      <jats:italic>Arabidopsis thaliana<\/jats:italic>\n                      ,\n                      <jats:italic>Fagopyrum esculentum<\/jats:italic>\n                      ,\n                      <jats:italic>Solanum lycopersicum<\/jats:italic>\n                      ,\n                      <jats:italic>Phalaenopsis equestris<\/jats:italic>\n                      , and\n                      <jats:italic>Zea mays<\/jats:italic>\n                      ) to identify genes with consistently low expression variation across organs, developmental stages, and environmental conditions. We identified 672 orthogroups that are universally stable across angiosperms; these are predominantly single-copy genes enriched for fundamental cellular functions including DNA repair, mRNA splicing, and translation. Validation using independent datasets and additional species confirmed that stability is maintained across diverse genotypes, conditions, and species. SEGs tend to be longer, have more exons, and exhibit lower GC content than other expressed genes. Using multiomics information available for\n                      <jats:italic>Arabidopsis<\/jats:italic>\n                      , we also explored epigenetic and functional characteristics associated with stability. Loss-of-function mutations in SEGs result in lethality far more frequently than in ubiquitously expressed genes, and protein abundance is similarly stable. SEGs have a significantly higher level of gene body methylation and H3K4me1 marks.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results reveal several genomic and epigenetic features that distinguish SEGs from ubiquitously expressed genes. They also suggest that SEG stability is not governed by specific regulatory motifs, but is rather \u201cby default\u201d state driven by a distinctive chromatin architecture.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1846139","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T06:56:32Z","timestamp":1786949792000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Calm in the midst of the storm: inferring gene expression stability in flowering plants"],"prefix":"10.3389","volume":"17","author":[{"given":"Anna V.","family":"Klepikova","sequence":"first","affiliation":[{"name":"Center of Bio- and Medical Technology","place":["Moscow, Russia"]},{"name":"Laboratory of Plant Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra M.","family":"Kasianova","sequence":"additional","affiliation":[{"name":"Center of Bio- and Medical Technology","place":["Moscow, Russia"]},{"name":"Laboratory of Plant Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artem S.","family":"Kasianov","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto","place":["Vair\u00e3o, Portugal"]},{"name":"Biopolis Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o","place":["Vair\u00e3o, Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksey A.","family":"Penin","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria D.","family":"Logacheva","sequence":"additional","affiliation":[{"name":"Center of Bio- and Medical Technology","place":["Moscow, Russia"]},{"name":"Laboratory of Plant Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"3543","DOI":"10.1105\/tpc.109.069153","article-title":"B-function expression in the flower center underlies the homeotic phenotype of Lacandonia schismatica (Triuridaceae)","volume":"22","author":"\u00c1lvarez-Buylla","year":"2010","journal-title":"Plant Cell"},{"key":"B2","unstructured":"Bigwigtobedgraph\n          \n          2026"},{"key":"B3","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s12859-021-04556-z","article-title":"ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes","volume":"23","author":"Anand","year":"2022","journal-title":"BMC Bioinf."},{"key":"B4","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"5245","DOI":"10.1158\/0008-5472.CAN-04-0496","article-title":"Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets","volume":"64","author":"Andersen","year":"2004","journal-title":"Cancer Res."},{"key":"B6","unstructured":"Trim Galore!\n          \n          2026"},{"key":"B7","unstructured":"Cordon: Codon Usage Analysis and Prediction of Gene Expressivity\n          \n          2026"},{"key":"B8","unstructured":"Venn Diagram\n          \n          2026"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.cell.2007.12.014","article-title":"High-resolution mapping and characterization of open chromatin across the genome","volume":"132","author":"Boyle","year":"2008","journal-title":"Cell."},{"key":"B11","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/ng.3149","article-title":"The genome sequence of the orchid Phalaenopsis equestris","volume":"47","author":"Cai","year":"2015","journal-title":"Nat. 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