Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ have been hindered by a lack of robust methods to profile comprehensive Ψ maps. Here we utilize bisulfite-induced deletion sequencing to generate transcriptome-wide Ψ maps at single-base resolution across various plant species. Integrating ribosomal RNA, transfer RNA and messenger RNA Ψ stoichiometry with mRNA abundance and polysome profiling data, we uncover a multilayered regulation of translation efficiency through Ψ modifications. rRNA pseudouridylation could globally control translation, although the effects vary at different rRNA Ψ sites. Ψ in the tRNA T-arm loop shows strong positive correlations between Ψ stoichiometry and the translation efficiency of their respective codons. We observed a general inverse correlation between Ψ level and mRNA stability, but a positive correlation with translation efficiency in Arabidopsis seedlings. In conclusion, our study provides critical resources for Ψ research in plants and proposes prevalent translation regulation through rRNA, tRNA and mRNA pseudouridylation.

Transcription activation is tightly associated with the openness of chromatin and allows direct contact between transcriptional regulators and their targeted DNA for gene expression. However, there are limited studies on the annotation of open chromatin regions (OCRs) in rice (Oryza sativa), especially those in reproductive organs. Here, we characterized OCRs in rice pistils and anthers with an assay for transposase-accessible chromatin using sequencing. Despite a large overlap, we found more OCRs in pistils than in anthers. These OCRs were enriched in gene transcription start sites (TSSs) and showed tight associations with gene expression. Transcription factor (TF) binding motifs were enriched at these OCRs as validated by TF chromatin immunoprecipitation followed by sequencing. Pistil-specific OCRs provided potential regulatory networks by binding directly to the targets, indicating that pistil-specific OCRs may be indicators of cis-regulatory elements in regulating pistil development, which are absent in anthers. We also found that open chromatin of pistils and anthers responded differently to low temperature (LT). These data offer a comprehensive overview of OCRs regulating reproductive organ development and LT responses in rice.

An acidic polysaccharide, named LAP-1, was extracted and isolated from Leonurus artemisia (Laur.), and was further purified with ion exchange chromatography and gel chromatography. The extraction conditions of the crude polysaccharides were optimized by single-factor experiments and response surface methodology. The primary structure of the purified polysaccharide was measured by FT-IR, GC-MS, and NMR. The results showed that LAP-1 was mainly composed of galacturonic acid (GalA), mannose (Man), xylose (Xyl), rhamnose (Rha), arabinose (Ara), glucose (Glc), galactose (Gal), fucose (Fuc), ribose (Rib), and glucuronic acid (GlcA) in the molar ratio of 8.74 : 3.45 : 1.02 : 1 : 2.11 : 5.60 : 4.73 : 1.08 : 1.09 : 1.47. Primary structure analysis results indicated that LAP-1 contained characteristic glycosyl linkages such as →1)-α-D-Manp, →1)-α-D-Glcp, →1)-α-D-Arap-(2→, →1)-β-D-Galp-(3→, →1)-β-D-Manp-(4→, →1)-β-D-Galp-(4→, →1)-β-D-Glcp-(4→, →1)-β-D-GalAp-(4→, →1)-β-D-GlcAp-(4→, →1)-β-D-Manp-(4,6→, →1)-β-D-Manp-(3,4→. The M_w/M_n (PDI), M_n, M_z and M_w of LAP-1 were determined to be 1.423, 6.979 × 10³ g mol⁻¹, 1.409 × 10⁴ g mol⁻¹, and 9.930 × 10³ g mol⁻¹ by HPSEC-MALLS-RID and DLS. SEM, TEM and AFM results indicated that LAP-1 was a highly branched structure. LAP-1 showed mild anticoagulant activity, low toxicity, and less spontaneous bleeding compared with heparin sodium. These results demonstrated the effective coagulation activity of Leonurus artemisia polysaccharides. Thus, the purified LAP-1 could be explored as a promising anticoagulant agent for the treatment of coagulation disorders.

The GRAS transcription factors play an indispensable role in plant growth and responses to environmental stresses. The GRAS gene family has extensively been explored in various plant species; however, the comprehensive investigation of GRAS genes in white lupin remains insufficient. In this study, bioinformatics analysis of white lupin genome revealed 51 LaGRAS genes distributed into 10 distinct phylogenetic clades. Gene structure analyses revealed that LaGRAS proteins were considerably conserved among the same subfamilies. Notably, 25 segmental duplications and a single tandem duplication showed that segmental duplication was the major driving force for the expansion of GRAS genes in white lupin. Moreover, LaGRAS genes exhibited preferential expression in young cluster root and mature cluster roots and may play key roles in nutrient acquisition, particularly phosphorus (P). To validate this, RT‐qPCR analysis of white lupin plants grown under +P (normal P) and −P (P deficiency) conditions elucidated significant differences in the transcript level of GRAS genes. Among them, LaGRAS38 and LaGRAS39 were identified as potential candidates with induced expression in MCR under −P. Additionally, white lupin transgenic hairy root overexpressing OE‐LaGRAS38 and OE‐LaGRAS39 showed increased root growth, and P concentration in root and leaf compared to those with empty vector control, suggesting their role in P acquisition. We believe this comprehensive analysis of GRAS members in white lupin is a first step in exploring their role in the regulation of root growth, tissue development, and ultimately improving P use efficiency in legume crops under natural environments.