Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants
Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatia...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1185377/full |
| _version_ | 1797744491026710528 |
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| author | Ce Chen Yining Ge Lingli Lu Lingli Lu |
| author_facet | Ce Chen Yining Ge Lingli Lu Lingli Lu |
| author_sort | Ce Chen |
| collection | DOAJ |
| description | Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research. |
| first_indexed | 2024-03-12T15:10:25Z |
| format | Article |
| id | doaj.art-b080afffb34f4d319d7304503287e76c |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-12T15:10:25Z |
| publishDate | 2023-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-b080afffb34f4d319d7304503287e76c2023-08-11T17:49:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-08-011410.3389/fpls.2023.11853771185377Opportunities and challenges in the application of single-cell and spatial transcriptomics in plantsCe Chen0Yining Ge1Lingli Lu2Lingli Lu3Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, ChinaMinistry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, ChinaMinistry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, ChinaKey Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, ChinaSingle-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.https://www.frontiersin.org/articles/10.3389/fpls.2023.1185377/fullsingle-cell transcriptomicsspatial transcriptomicssingle-nucleus RNA-seqsingle-cell RNA-seqprotoplast |
| spellingShingle | Ce Chen Yining Ge Lingli Lu Lingli Lu Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants Frontiers in Plant Science single-cell transcriptomics spatial transcriptomics single-nucleus RNA-seq single-cell RNA-seq protoplast |
| title | Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants |
| title_full | Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants |
| title_fullStr | Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants |
| title_full_unstemmed | Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants |
| title_short | Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants |
| title_sort | opportunities and challenges in the application of single cell and spatial transcriptomics in plants |
| topic | single-cell transcriptomics spatial transcriptomics single-nucleus RNA-seq single-cell RNA-seq protoplast |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1185377/full |
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