Project description:The transition of chloroplast function from biogenesis to degeneration upon leaf senescence is critical for a plant’s fitness, as nutrient relocation from leaves to reproductive organs is achieved through this process. The optimal timing of transition should be regulated by tight coordination between chloroplast and nucleus, but the underlying mechanisms remain elusive. Here, we describe the regulatory mechanism of this transition. Chloroplast-Related LONG NONCODING RNA 1 (CHLORELLA1) is highly co-expressed with genes coding for chloroplast functionality during leaf development. Leaves of chlorella exhibit precocious senescence symptoms and a decline in the expression of chloroplast-associated genes, indicating that CHLORELLA1 plays a role in maintaining chloroplast function. Mechanistically, nucleus-encoded CHLORELLA1 transcripts are translocated into the chloroplast and contribute to the assembly of the plastid-encoded RNA polymerase (PEP) complex. At aged leaves, decreased expression of CHLORELLA1 attenuates PEP complex assembly and transcription of photosynthesis genes, possibly triggering leaf senescence. Moreover, CHLORELLA1 is directly activated by GLK1/2, master regulators of chloroplast maintenance. Our study unravels a new layer of the regulation via chloroplast-targeted lncRNA as an anterograde signal in timely decision of leaf senescence.
2025-08-16 | GSE255867 | GEO
Project description:Senecio squalidus genome, dovetail data
Project description:In this study, we have characterized a putative chloroplast ribosome assembly factor. To elucidate transcriptional responses caused by decreased chloroplast function, we have measured the transcriptome of wild-type and knock-down seedlings.
Project description:The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.
Project description:Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.
