Lingjuan Xie

MicroRNAs (miRNAs) are a class of small, non‐coding RNAs that regulate gene expression in eukaryotes. Among them, miR396 targets GROWTH‐REGULATING FACTOR (GRF) transcription factors and forms one of the most highly conserved regulatory modules in plants. Recent studies have greatly expanded the functional landscape of the miR396–GRF module, showing that, beyond its canonical role in leaf morphogenesis, it also participates in root meristem regulation, reproductive development, yield formation, tissue regeneration, and responses to diverse abiotic and biotic stresses. In crop plants, this module further controls agronomically important traits. Here, we summarize current knowledge of the evolutionary conservation and diversification of the MIR396 loci, the upstream pathways that control miR396 expression, and the developmental and stress‐related outputs mediated by the miR396–GRF module. We also discuss evidence that miR396 functions as a context‐dependent regulator rather than a simple growth suppressor, and highlight how precise manipulation of the miR396–GRF module may provide new opportunities for crop improvement by optimizing growth, regeneration, and stress resilience.

Crabgrasses (Digitaria spp.) rank among the most invasive upland weeds globally, exhibiting remarkable ecological plasticity. To uncover the genomic basis underlying their weediness and environmental adaptability, we generate a telomere-to-telomere (T2T) reference genome of Digitaria sanguinalis, along with its diploid progenitor D. radicosa and tetraploid progenitor D. milanjiana. In addition, we re-sequence 579 accessions collected from fields of 24 grain-producing provinces in China. A phenotypic classification system for Digitaria species is developed by integrating genome-scale data with detailed morphological observations. Phylogenomic and comparative genomic analyses resolve the evolutionary history of Digitaria and reveal lineage-specific expansions in herbicide-associated gene families. Extensive sympatric introgression is observed within Digitaria, correlated with environmental selection. Through dose-response assay of 196 accessions, we identify 19 candidate genes associated with herbicide resistance, including DsSOH1. Haplotype analysis indicates that the resistant allele at DsSOH1 locus originated from D. ciliaris, suggesting a possible evolutionary contribution of introgression to the distribution of resistance-associated alleles. Together, our findings provide genomic insights into the evolutionary success of D. sanguinalis and offer resources for studying polyploid evolution and environmental adaptation as well as precision weed management in agroecosystems.

Crabgrasses ( Digitaria spp.), the most problematic upland weeds, are well-documented for their broad-spectrum herbicide resistance and ecological adaptability. The genetic mechanism of these adaptive traits remains largely unexplored. We assembled three telomere-to-telomere (T2T) reference genomes of the globally invasive species Digitaria sanguinalis , along with its diploid and tetraploid progenitors. In addition, we re-sequenced 579 accessions from sympatric populations sampled over the past decade, coupled with nicosulfuron (an ALS inhibitor herbicide) resistance phenotyping. Genomic analysis of D. sanguinalis revealed adaptation driven by polyploidization. Extensive sampling across Digitaria species uncovered widespread introgression among sympatric lineages. Notably, introgression contributed to enhanced cold tolerance, likely facilitating adaptation to northern environments. Dose-response assays revealed a recent surge in nicosulfuron resistance in D. sanguinalis , which cannot be explained by target-site mutations alone. Genome-wide association study identified 40 SNPs significantly associated with non-target-site resistance (NTSR). We further identified a recently introgressed region from sympatric D. ciliaris associated with NTSR. Moreover, herbicide-resistant populations exhibited a higher number of introgressed genomic blocks compared to susceptible ones. These findings reveal adaptive introgression from relatives as a key source of variation, promoting rapid adaptation under selection pressure.

: Understanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Through de novo annotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats ( sati ). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model for Arabidopsis centromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.