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Abstract Background Waterlogging stress (WS) negatively impacts crop growth and productivity, making it important to understand crop resistance processes and discover useful WS resistance genes. In this study, rye cultivars and wild rye species were subjected to 12-day WS treatment, and the cultivar Secale cereale L. Imperil showed higher tolerance. Whole transcriptome sequencing was performed on this cultivar to identify differentially expressed (DE) messenger RNAs (DE-mRNAs) and long non-coding RNAs (DE-lncRNAs) involved in WS response. Results Among the 6 species, Secale cereale L. Imperil showed higher tolerance than wild rye species against WS. The cultivar effectively mitigated oxidative stress, and regulated hydrogen peroxide and superoxide anion. A total of 728 DE-mRNAs and 60 DE-lncRNAs were discovered. Among these, 318 DE-mRNAs and 32 DE-lncRNAs were upregulated, and 410 DE-mRNAs and 28 DE-lncRNAs were downregulated. GO enrichment analysis discovered metabolic processes, cellular processes, and single-organism processes as enriched biological processes (BP). For cellular components (CC), the enriched terms were membrane, membrane part, cell, and cell part. Enriched molecular functions (MF) terms were catalytic activity, binding, and transporter activity. LncRNA and mRNA regulatory processes were mainly related to MAPK signaling pathway-plant, plant hormone signal transduction, phenylpropanoid biosynthesis, anthocyanin biosynthesis, glutathione metabolism, ubiquitin-mediated proteolysis, ABC transporter, Cytochrome b6/f complex, secondary metabolite biosynthesis, and carotenoid biosynthesis pathways. The signalling of ethylene-related pathways was not mainly dependent on AP2/ERF and WRKY transcription factors (TF), but on other factors. Photosynthetic activity was active, and carotenoid levels increased in rye under WS. Sphingolipids, the cytochrome b6/f complex, and glutamate are involved in rye WS response. Sucrose transportation was not significantly inhibited, and sucrose breakdown occurs in rye under WS. Conclusions This study investigated the expression levels and regulatory functions of mRNAs and lncRNAs in 12-day waterlogged rye seedlings. The findings shed light on the genes that play a significant role in rye ability to withstand WS. The findings from this study will serve as a foundation for further investigations into the mRNA and lncRNA WS responses in rye.

MYB is a common transcription factors widely involved in the regulation of anthocyanidin biosynthesis. In order to explore the regulatory role of MYB transcription factors in the biosynthesis of common buckwheat anthocyanidins, we screened and cloned a MYB gene associated with anthocyanin biosynthesis from the transcriptomic data of common buckwheat varieties of safflower common buckwheat and Beizaosheng, and named it FeR2R3-MYB, GenBank login number was MT151381.1. The sequence was analyzed by bioinformatics analysis and qRT-PCR was used to analyze the expression characteristics of FeR2R3-MYB gene in Beizaosheng and safflower common buckwheat. The results were as follows: (1) FeR2R3-MYB gene was 831 bp in total length, encoding 276 amino acids. The relative molecular mass of the protein was 30.95 kD, the theoretical isoelectric point (pI) was 8.73, and the instability index of the protein was 69.64, which belonged to the unstable protein. The total hydrophobic value was -0.679, and the whole peptide chain showed hydrophilic characteristics. (2) FeR2R3-MYB had a typical R2R3-MYB domain and belonged to the R2R3-MYB subfamily. (3) FeR2R3-MYB was closely related to common buckwheat and knotweed, belonging to the same family. (4) The promoter sequence of FeR2R3-MYB contained a total of nine light corresponding elements, 12 transcription factor binding sites, four abiotic corresponding elements and two hormone response elements. (5) Subcellular localization found that FeR2R3-MYB was only expressed in the nucleus. (6) The expression of FeR2R3-MYB gene of safflower common buckwheat was higher than that of Beizaosheng in leaves and inflorescences, and it was further speculated that FeR2R3-MYB gene could positively regulate the biosynthesis of common buckwheat anthocyanin. In summary, these results lay a foundation for further deepening the research on the function and expression regulation of FeR2R3-MYB gene in the biosynthetic pathway of common buckwheat anthocyanin.