The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses. Overall, 5mC represses the DNA binding of AtWOX14 monomers but facilitates the binding of its dimers, and the methylation effect on a cytosine’s affinity to AtWOX14 is position-dependent. Notably, we found that the most preferred homodimeric configuration of AtWOX14 has changed from ER1 to ER0 upon methylation. This change has the potential to rewire the regulatory network downstream of AtWOX14, as suggested by the GO analyses and the strength changes in the DAP-seq peaks upon methylation. Therefore, this work comprehensively illustrates the specificity and targets of AtWOX14 and reports a previously unrecognized effect of DNA methylation on transcription factor binding.

Giant reed (Arundo donax) is widely distributed across the globe and is considered an important energy crop. This study presents the first comprehensive analysis of the chloroplast genome of giant reed, revealing detailed characteristics of this species’ chloroplast genome. The chloroplast genome has a total length of 137,153 bp, containing 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, with a GC content of 39%. Functional analysis indicates that a total of 45 photosynthesis-related genes and 78 self-replication-related genes were identified, which may be closely associated with its adaptability and growth characteristics. Phylogenetic analysis confirmed that Arundo donax cv. Lvzhou No.1 belongs to the Arundionideae clade and occupies a distinct evolutionary position compared to other Arundo species. The findings of this study not only enhance our understanding of the giant reed genome but also provide valuable genetic resources for its application in biotechnology, bioenergy crop development, and ecological restoration.

Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance; however, the molecular mechanisms governing stalk development in pearl millet remain to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined four developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that two co-expression modules together with candidate genes were involved in stalk elongation and the thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement in pearl millet.

Tripsacum laxum (Guatemalan grass) is a perennial fodder grasses, which is commonly growing in large parts of Africa for a source of livestock feed. It has a high economic value as a forage. In this study, we obtained a complete chloroplast genome of T. laxum by Illumina sequencing. The results showed a circular genome of 140,556 bp, including the large single copy region (LSC, 82,939 bp), the small single-copy region (SSC, 12,573 bp), and a pair of 22,522 bp inverted repeat regions (IRs). The circular genome contained 120 genes, including 74 protein-coding genes, eight ribosomal RNA genes and 38 tRNA genes. Evolutionary relationship analysis indicates that T. laxum is more closely related to previously reported T. dactyloides.

Giant Juncao (Cenchrus fungigraminus) is a perennial C4 forage and bioenergy grass with high biomass productivity and strong tolerance to adverse environments. However, the transcriptional regulatory mechanisms underlying its stress adaptation remain poorly understood. WRKY transcription factors are key regulators of plant stress responses, but their genomic features and functional potential in this species have not been systematically investigated. Here, we identified 182 CfWRKY genes and classified them into three major groups based on phylogenetic relationships. Comprehensive analyses of their chromosomal distribution, gene structures, conserved motifs, cis-regulatory elements, and duplication patterns revealed that segmental duplication, alongside whole-genome duplication, was the primary force driving WRKY family expansion. Transcriptome analysis under salt treatments showed diverse and dynamic expression responses, with several CfWRKY genes exhibiting strong induction and early responsiveness. Weighted gene co-expression network analysis under drought and rehydration conditions further identified 31 stress-related modules and 27 CfWRKY candidates potentially involved in water-deficit adaptation. This study presents the first genome-wide characterization of the WRKY family in Giant Juncao and provides integrative insights into their evolutionary patterns and stress-responsive regulatory roles. Our findings offer valuable candidate genes and a molecular basis for functional genomics and breeding of stress-resilient forage and energy grasses.