Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.

Background: Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the invasion of the common reed Phragmites australis , a grass species that became invasive in North America after its introduction from Europe, to elucidate the molecular mechanisms potentially underlying its invasion process. Results: By integrating single-cell RNA sequencing, spatial transcriptomics, and comparative genomics, we construct a single-cell atlas of Phragmites australis , and identify 19 transcriptionally distinct cell types, including meristematic cells, parenchyma, mesophyll, epidermal, and vascular tissues. Comparative analysis of common garden-grown native populations from Europe and invasive populations from North America reveals a significant proportion of differentially expressed genes located on B chromosomes, which show copy number expansion in invasive genomes. Four B-chromosome genes, PaChr24B.43 ( IMP-α3 ), PaChr24B.82 ( GATA2 ), PaChr24B.218 ( SCC3 ), and PaChr24B.240 ( SCC3 ), are consistently differentially expressed between invasive and noninvasive populations across nearly all cell types. At the tissue level, mesophyll, parenchyma, vascular, and epidermal cells in the invasive population all exhibit increased gene expression in response to sugar starvation and light deprivation. Epidermal cells also show strong activated gene expression in response to hypoxia but suppressed expression of genes involved in the defence related respiratory burst. Conclusions: This study establishes a cell type-resolved molecular atlas of a nonmodel invasive plant and reveals cell type-specific gene regulatory mechanisms within the regenerative shoot system. These findings advance our understanding of the cellular and genomic basis of plant invasiveness and provide a foundation for future ecological research and management.

Compared with rose, chrysanthemum, and water lily, the absence of short-wide and long-narrow tepals of ornamental lotus (Nelumbo Adans.) limits the commercial value of flowers. In this study, the genomes of two groups of lotus mutants with wide-short and narrow-long tepals were resequenced to uncover the genomic variation and candidate genes associated with tepal shape. In group NL (short for N. lutea, containing two mutants and one control of N. lutea), 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained, while 639,953 SNPs and 134,6118 Indels were obtained in group WSH (short for ‘Weishan Hong’, containing one mutant and two controls of N. nucifera ‘Weishan Hong’). Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4890 (NL group) and 1272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (p < 0.05). Finally, there were 306 candidate genes that were sieved to determine the development of tepal shape in lotus plants. It will be an essential reference for future identification of tepal-shaped control genes in lotus plants. This is the first comprehensive report of genomic variation controlling tepal shape in lotus, and the mutants in this study are promising materials for breeding novel lotus cultivars with special tepals.