Spatially resolved transcriptomic analysis of the germinating barley grain

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(15), P. 7798 - 7819

Published: June 23, 2023

Seeds are a vital source of calories for humans and unique stage in the life cycle flowering plants. During seed germination, embryo undergoes major developmental transitions to become seedling. Studying gene expression individual cell types has been challenging due lack spatial information or low throughput existing methods. To overcome these limitations, transcriptomics workflow was developed germinating barley grain. This approach enabled high-throughput analysis expression, revealing specific patterns various functional categories at sub-tissue level. study revealed over 14 000 genes differentially regulated during first 24 h after imbibition. Individual genes, such as aquaporin family, starch degradation, wall modification, transport processes, ribosomal proteins transcription factors, were found have time. Using autocorrelation algorithms, we identified auxin that had increasingly focused within subdomains time, suggesting their role establishing axis. Overall, our provides an unprecedented spatially resolved cellular map germination identifies genomics targets better understand restricted processes germination. The data can be viewed https://spatial.latrobe.edu.au/.

Language: Английский

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Understanding plant pathogen interactions using spatial and single-cell technologies

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Aug. 4, 2023

Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted identification of multiple immune receptors model crop species as well signaling overlap surface-localized intracellular receptors. However, scientists still have a limited understanding how plants respond to spatial cellular resolution. Recent advancements single-cell, single-nucleus technologies can now be applied plant-pathogen interactions. Here, we outline current state these highlight outstanding biological questions that addressed future.

Language: Английский

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Chromosome-level genomes of three key Allium crops and their trait evolution

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(11), P. 1976 - 1986

Published: Nov. 1, 2023

Language: Английский

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Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics Technologies

Glomerular Diseases, Journal Year: 2024, Volume and Issue: 4(1), P. 49 - 63

Published: March 13, 2024

Background: The first spatially resolved transcriptomics platforms, GeoMx (Nanostring) and Visium (10x Genomics) were launched in 2019 recognized as the method of year by Nature Methods 2020. subsequent refinement expansion these other technologies to increase -plex, work with formalin-fixed paraffin-embedded tissue, analyze protein addition gene expression have only added their significance impact on biomedical sciences. In this perspective, we focus two platforms for spatial transcriptomics, Visium, how been used provide novel insight into kidney disease. choice platform will depend largely experimental questions design. application clinically sourced biopsies presents opportunity identify specific tissue biomarkers that help define disease etiology more precisely target therapeutic interventions future. Summary: review, a description existing emerging can be capture data from tissue. These provided new heterogeneity diseases, reactions are distributed within which cells affected, molecular pathways predict response therapy. Key Message: upcoming years see intense use better pathophysiology diseases develop diagnostic tests guide personalized treatments patients.

Language: Английский

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A spatial transcriptome map of the developing maize ear

Nature Plants, Journal Year: 2024, Volume and Issue: 10(5), P. 815 - 827

Published: May 14, 2024

Language: Английский

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