Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Март 14, 2023

Abstract Background The epidermis of cotton ovule produces fibers, the most important natural cellulose source for global textile industry. However, molecular mechanism fiber cell growth is still poorly understood. Results Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) ATAC (scATAC-seq) to systematically characterize cells outer integument ovules from wild type fuzzless/lintless ( fl ) (Gossypium hirsutum ). By jointly analyzing scRNA-seq data wildtype fl, identify five populations including construct development trajectory lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, demonstrate that primary a highly regulated circadian rhythmic process. Moreover, small peptide GhRALF1 rhythmically controls possibly through oscillating auxin signaling proton pump activity in plasma membrane. Combining with scATAC-seq, further two cardinal cis-regulatory elements (CREs, TCP motif, TCP-like motif) which are bound trans factors GhTCP14s modulate metabolism mitochondria protein translation regulating approximately one third genes expressed Conclusions We uncover fiber-specific clock-controlled gene expression program growth. This study unprecedentedly reveals new route improve traits engineering clock

Язык: Английский

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Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100630 - 100630

Опубликована: Май 25, 2023

Taxus leaves provide the raw industrial materials for taxol, a natural antineoplastic drug widely used in treatment of various cancers. However, precise distribution, biosynthesis, and transcriptional regulation taxoids other active components remain unknown. Matrix-assisted laser desorption/ionization-mass spectrometry imaging analysis was to visualize secondary metabolites leaf sections mairei, confirming tissue-specific accumulation different metabolites. Single-cell sequencing produce expression profiles 8846 cells, with median 2352 genes per cell. Based on series cluster-specific markers, cells were grouped into 15 clusters, suggesting high degree cell heterogeneity T. mairei leaves. Our data create first metabolic single-cell atlas reveal spatial temporal patterns several pathways. According cell-type annotation, most taxol biosynthesis are expressed mainly mesophyll cells; phenolic acid flavonoid highly epidermal (including stomatal complex guard cells); terpenoid steroid specifically cells. A number novel cell-specific transcription factors involved metabolite identified, including MYB17, WRKY12, WRKY31, ERF13, GT_2, bHLH46. research establishes landscape major types at resolution provides valuable resources studying basic principles cell-type-specific metabolism.

Язык: Английский

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Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells

Molecular Plant, Год журнала: 2023, Номер 16(12), С. 1990 - 2003

Опубликована: Окт. 17, 2023

Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at cellular level remain largely elusive. In this study, we employed single-cell RNA sequencing comprehensively characterize transcriptome profile cotton leaves and established hierarchical transcriptional network regulating cell-specific production. We observed substantial expression levels genes associated with both volatile terpenes (such as β-caryophyllene β-myrcene) non-volatile gossypol-type secretory glandular cells. Moreover, two novel transcription factors, namely GoHSFA4a GoNAC42, are identified function downstream Gossypium PIGMENT GLAND FORMATION genes. Both factors could directly regulate biosynthetic cells developmental stimuli. For convenient retrieval data generated developed user-friendly web server . Our findings not only offer valuable insights into precise regulation but also provide potential targets for breeding endeavors.

Язык: Английский

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The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Cell Reports, Год журнала: 2024, Номер 43(2), С. 113747 - 113747

Опубликована: Фев. 1, 2024

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development response to bacteria, but the transcriptional reprogramming occurs these root cells remains largely uncharacterized. Here, we describe cell-type-specific transcriptome of Medicago truncatula during early nodule wild-type genotype Jemalong A17, complemented hypernodulating mutant (sunn-4) expand cell population responding infection and subsequent biological inferences. The analysis identifies epidermal hair stele sub-cell types associated regulation proliferation. Trajectory inference shows cortex-derived lineages differentiating form primordia and, posteriorly, its meristem, while modulating phytohormone-related genes. Gene regulatory transcriptomes new regulators nodulation, including STYLISH 4, for which function is validated.

Язык: Английский

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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

BioDesign Research, Год журнала: 2024, Номер 6, С. 0029 - 0029

Опубликована: Янв. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Язык: Английский

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