The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

Pennisetum species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote the preservation and utilization of ornamental Pennisetum resources, we developed simple sequence repeat (SSR) markers from the Pennisetum setaceum cv. ‘Rubrum’ transcriptome and verified their conservation in 38 sources. Our transcriptome sequencing efforts generated 58.91 Gb of clean data containing 55,627 unigenes. We functionally annotated 30,930 unigenes, with functions enriched in translation and ribosomal structure and biogenesis. Database comparisons indicated that the closest relative of P. setaceum cv. ‘Rubrum’ is Setaria italica. Over five thousand SSR markers were detected in the transcriptomic data. We selected 38 pairs of highly polymorphic SSR markers from 50 randomly selected SSR markers. Based on genetic diversity analysis of 38 ornamental Pennisetum sources, we obtained 312 polymorphic bands, with an average of 8.21 alleles per primer. Principal coordinate analyses and generation of a, which proved that Pennisetum has moderate genetic diversity. In addition, fingerprint maps were constructed to improve Pennisetum identification. The transcriptome data generated by our study enhances the transcriptional information available for P. setaceum. This study lays the foundation for the collection and utilization of ornamental Pennisetum resources and provides a basis for future breeding projects using this species.

Zoysia japonica is an important warm-season turfgrass used worldwide. The decreased aesthetic quality and functionality during leaf senescence hamper its further utilization. However, information about the transcriptional mechanism and genes involved in leaf senescence in Z. japonica needs to be more extensive. Therefore, to better understand leaf senescence in Z. japonica, we investigated the integrated analysis of chlorophyll fluorescence test (JIP-test) and RNA sequencing (RNA-seq) of mature and senescent leaves. First, we identified 22,049 genes, of which 4038 were differentially expressed genes (DEGs). The results for gene expression profiles were evaluated using quantitative real-time PCR. A total of 2515 genes have homologous genes in other plants. The matched known-function SAGs are mainly involved in chlorophyll degradation and plant hormone response. A total of 539 differentially expressed transcription factor genes, including AP2/ERF-ERF, NAC, WRKY, bHLH, and MYB, were identified to be associated with leaf senescence. Next, senescence represses chlorophyll biosynthesis while upregulating chlorophyll degradation. Senescence harms the integrity and functionality of PSII, PSI, and the intersystem electron transport chain. In addition, IAA biosynthesis was inhibited, whereas ABA and ET biosynthesis were activated in leaf senescence, and senescence activates signal transduction of IAA, ABA, and ET. These findings add to our understanding of the regulatory mechanism of leaf senescence. The senescence-associated genes are candidate targets for providing new insight into leaf senescence modeling in Z. japonica. They provided a theoretical foundation to reveal the functions of senescence-associated genes and chlorophyll catabolic genes involved in leaf senescence.

Carex is among the most species-rich genera of angiosperms and plays important ecological roles in wetlands, alpine regions, and temperate ecosystems worldwide. However, research on this genus has long been challenged by pronounced phenotypic plasticity, reduced floral morphology, frequent hybridization, and complex chromosomal evolution. Although recent advances in molecular phylogenetics, comparative genomics, reproductive biology, and ecophysiology have substantially expanded the knowledge of Carex, these findings remain fragmented across disciplines. Here, we synthesize current evidence on Carex taxonomy and phylogeny, genomic and karyotypic evolution, reproductive and life history strategies, abiotic stress responses, ecosystem functions, and bioresource potential within a cross-scale framework. This review emphasizes how genomic architecture, life history variation, and ecophysiological adaptation jointly shape species diversification and ecosystem functioning, while clarifying their implications for habitat restoration and the sustainable use of Carex resources. Finally, we identify key priorities for future research, including improved phylogenomic resolution, comparative functional studies, climate-resilience assessment, and germplasm conservation and sustainable use.