Project description:Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues. Four RNA pools were created corresponding to four different tissues: root, leaf, stem, spica (tassel) at developmental stage, then each pool was sequenced.
Project description:This high-throughput sequencing submission contains H3K27ac CUT&Tag data used to build a source-supported regulatory atlas for foxtail millet, Setaria italica, and a single Setaria viridis validation sample used for representative candidate loci. The data support an H3K27ac-associated regulatory map, sequence-model based candidate cis-regulatory region prediction, and conservative candidate-locus prioritization.
Project description:Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture often facing various adversities, it’s urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level.
Project description:In Setaria italica (foxtail millet), SiUBC39 is implicated in regulating key agronomic traits, including plant height, flowering time, and stress tolerance. To elucidate the molecular mechanisms underlying SiUBC39’s roles in these traits, we affinity-purified SiUBC39-GFP and the corresponding GFP control protein via immunoprecipitation (IP). The immunoprecipitated complexes were then subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify proteins interacting with SiUBC39.
Project description:Shotgun analysis was employed to obtain the proteome of two foxtail millet (Setaria italica) varieties, Ci846 and Yugu18, at the jointing stage. Whole proteins were extracted from internodes, nodes, and leaves, respectively. Eluted peptides were analyzed using a Q Exactive HF instrument (Thermo Fisher, USA).
Project description:N6-methyladenosine (m6A) is a pivotal epitranscriptomic modification that regulates mRNA metabolism and plays critical roles in plant growth and environmental responses. However, the evolution and roles of m6A modifications in plant domestication remain largely unexplored. This study combined RNA-seq and MeRIP-seq data to compare m6A modifications profiles between foxtail millet (Setaria italica, Yugu1) and its wild ancestor S. viridis (A10). Peak calling analysis identified 6,928 m6A peaks associated with 6,407 protein-coding genes in Yugu1 and 6,274 m6A peaks in 5,858 genes in A10, respectively. Comparative analysis revealed numerous differentially expressed genes (DEGs) and differentially methylated peaks (DMPs), whose functions were elucidated by GO and KEGG enrichment analyses. Integration of DMPs paired with DEGs, we found 209 hyper-methylated peaks associated with upregulated transcription levels, and 90 hypo-methylated peaks associated with downregulated transcription levels. This dataset provides valuable resource for further investigating the roles of m⁶A modification in crop domestication.
