Abstract
• This study presents the first single-cell and spatial transcriptomic resource for loquat shoot apices during the vegetative-to-reproductive transition. • Epidermal and shoot meristematic cells exhibited the most pronounced transcriptional changes, suggesting their crucial roles in floral initiation. • A total of 43 candidate genes were identified as key regulators in the initiation of floral bud differentiation in loquat shoot apices, driven by a coordinated network of photoperiod- and circadian rhythm-related genes. Flowering time and subsequent fruiting significantly influence the economic value of fruit trees. However, the regulatory mechanisms underlying the vegetative-to-reproductive transition remain understudied, particularly at single-cell and spatial levels. Here, we present a single-nucleus (snRNA-seq) and spatial transcriptomic (stRNA-seq) atlas of shoot apices in loquat ( Eriobotrya japonica ), a perennial fruit crop with both nutritional and medicinal importance. From the snRNA-seq dataset, 42,546 nuclei were profiled and resolved into 22 clusters corresponding to seven major cell types. Pseudotime analysis reconstructed developmental trajectories, revealing bifurcated lineages toward external and internal tissues, and identified genes dynamically associated with cell differentiation. Comparative analysis between the pre-initiation and onset stages of floral bud initiation uncovered 3,329 differentially expressed genes, including 67 homologs of Arabidopsis flowering-related genes, with the most pronounced transcriptional changes observed in epidermal and shoot meristematic cells, underscoring their central roles in floral initiation. Moreover, 43 key candidate genes, such as EjCRY2 and EjAGL79 , associated with pseudotime branch points critical for cell fate decisions were predicted to act within a regulatory network dominated by photoperiod- and circadian rhythm-related pathways. Finally, integration with stRNA-seq demonstrated well concordance with snRNA-seq results and supported cell-type annotations particularly for epidermal and shoot meristematic cells. Collectively, the marker genes and associated datasets generated here provide a valuable resource for advancing single-cell and spatial transcriptomic research in loquat and potentially other fruit tree species. In addition, the identified candidate genes represent promising targets for in-depth functional studies and for breeding strategies aimed at manipulating flowering and fruiting time in loquat.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by-nc-nd. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 10
Claim · model-written summary
The loquat shoot apex atlas resolved 42,546 nuclei into 22 clusters and seven major cell types.
- Outcome
- nuclei were profiled and resolved into 22 clusters corresponding to seven major cell typese0
- Value
- 42,546e0
Not reportedTaxon
Verbatim
e0“42,546 nuclei were profiled and resolved into 22 clusters corresponding to seven major cell types.”
Claim · model-written summary
Pseudotime reconstruction found bifurcated lineages toward external and internal tissues.
- Outcome
- bifurcated lineages toward external and internal tissuese0
Not reportedTaxon
Verbatim
e0“Pseudotime analysis reconstructed developmental trajectories, revealing bifurcated lineages toward external and internal tissues”
Claim · model-written summary
Pseudotime analysis identified genes dynamically associated with cell differentiation.
Not reportedTaxonDirection
Verbatim
e0“identified genes dynamically associated with cell differentiation”
Claim · model-written summary
The pre-initiation versus onset comparison found 3,329 differentially expressed genes.
Not reportedTaxon
Verbatim
e0“between the pre-initiation and onset stages of floral bud initiation uncovered 3,329 differentially expressed genes”
Claim · model-written summary
The differentially expressed genes included 67 Arabidopsis flowering gene homologs.
Not reportedTaxon
Verbatim
e0“including 67 homologs of Arabidopsis flowering-related genes”
Claim · model-written summary
Epidermal and shoot meristematic cells had the most pronounced transcriptional changes.
- Organ / stage
- epidermal and shoot meristematic cellse0
- Outcome
- transcriptional changese0
- Direction
- most pronouncede0
Not reportedTaxon
Verbatim
e0“most pronounced transcriptional changes observed in epidermal and shoot meristematic cells”
Claim · model-written summary
The analysis predicted 43 candidate genes associated with pseudotime branch points.
Not reportedTaxon
Verbatim
e0“43 key candidate genes, such as EjCRY2 and EjAGL79 , associated with pseudotime branch points critical for cell fate decisions were predicted”
Claim · model-written summary
The candidate genes were predicted to act in a photoperiod and circadian rhythm regulatory network.
Not reportedTaxon
Verbatim
e0“predicted to act within a regulatory network dominated by photoperiod- and circadian rhythm-related pathways”
Claim · model-written summary
Spatial transcriptomics agreed with single-nucleus results and supported epidermal and shoot meristematic cell annotations.
Not reportedTaxon
Verbatim
e0“integration with stRNA-seq demonstrated well concordance with snRNA-seq results and supported cell-type annotations particularly for epidermal and shoot meristematic cells”
Claim · model-written summary
The marker genes and datasets provide a loquat single-cell and spatial transcriptomic resource.
- Taxon
- loquat
Eriobotrya japonicae0 - Outcome
- valuable resourcee0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the marker genes and associated datasets generated here provide a valuable resource for advancing single-cell and spatial transcriptomic research in loquat”