Current status and trends in forest genomics DOI Creative Commons
Dulal Borthakur, Victor Busov, Hieu X. Cao

et al.

Forestry Research, Journal Year: 2022, Volume and Issue: 2(1), P. 0 - 0

Published: Jan. 1, 2022

Forests are not only the most predominant of Earth's terrestrial ecosystems, but also core supply for essential products human use. However, global climate change and ongoing population explosion severely threatens health forest ecosystem aggravtes deforestation degradation. Forest genomics has great potential increasing productivity adaptation to changing climate. In last two decades, field advanced quickly owing advent multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, spatial transcriptomes, as well bioinformatics analysis which have led generation multidimensional, multilayered, spatiotemporal gene expression data. These together with basic technologies routinely used in plant biotechnology, enable us tackle many important or unique issues biology, provide a panoramic view an integrative elucidation molecular regulatory mechanisms underlying phenotypic changes variations. this review, we recapitulated advancement current status 12 research branches genomics, then provided future directions focuses each area. Evidently, shift from simple biotechnology-based research, setup investigation interpretation development differentiation just begun emerge.

Language: Английский

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics DOI Creative Commons

Carolin Grones,

Thomas Eekhout, Dongbo Shi

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 812 - 828

Published: Jan. 17, 2024

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.

Language: Английский

Citations

25
Transcriptional landscape of highly lignified poplar stems at single-cell resolution DOI Creative Commons
Yang Chen, Shaofei Tong, Yuanzhong Jiang

et al.

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Nov. 22, 2021

Plant secondary growth depends on the activity of vascular cambium, which produces xylem and phloem. Wood derived from is most abundant form biomass globally has played key socio-economic subsistence roles throughout human history. However, despite intensive study development, full diversity cell types gene networks engaged are still poorly understood.

Language: Английский

Citations

84
FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants DOI Creative Commons
Yanping Long, Zhijian Liu, Jinbu Jia

et al.

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Feb. 19, 2021

Abstract The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite protoplasting that requires digesting cell walls from different types plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length at single-nucleus level using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, validate robustness this approach Arabidopsis root cells developing endosperm. Sequencing results demonstrate it allows uncovering alternative splicing polyadenylation-related isoform information level, which facilitates characterizing identities.

Language: Английский

Citations

79
Single-cell transcriptomics sheds light on the identity and metabolism of developing leaf cells DOI Open Access
Rubén Tenorio Berrío, Kevin Verstaen, Niels Vandamme

et al.

PLANT PHYSIOLOGY, Journal Year: 2021, Volume and Issue: 188(2), P. 898 - 918

Published: Oct. 19, 2021

Abstract As the main photosynthetic instruments of vascular plants, leaves are crucial and complex plant organs. A strict organization leaf mesophyll epidermal cell layers orchestrates photosynthesis gas exchange. In addition, water nutrients for growth transported through tissue. To establish single-cell transcriptomic landscape these different tissues, we performed high-throughput transcriptome sequencing individual cells isolated from young Arabidopsis (Arabidopsis thaliana) seedlings grown in two environmental conditions. The detection approximately 19,000 transcripts over 1,800 high-quality revealed 14 populations composing young, differentiating leaf. Besides comprising core identified subpopulations with a distinct identity or metabolic activity. proposed cell-type-specific markers each populations. Finally, an intuitive web tool allows browsing presented dataset. Our data present insights on how constituting developing connected via developmental, metabolic, stress-related trajectories.

Language: Английский

Citations

76
PlantscRNAdb: A database for plant single-cell RNA analysis DOI Creative Commons
Hongyu Chen, Xinxin Yin, Longbiao Guo

et al.

Molecular Plant, Journal Year: 2021, Volume and Issue: 14(6), P. 855 - 857

Published: May 4, 2021

Language: Английский

Citations

74
Vision, challenges and opportunities for a Plant Cell Atlas DOI Creative Commons
Jahed Ahmed,

Oluwafemi Alaba,

Gazala Ameen

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: Sept. 7, 2021

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, stewardship, energy, technology healthcare. This effort requires conceptual technological framework identify map all cell types, comprehensively annotate localization organization molecules at cellular tissue levels. framework, called Plant Cell Atlas (PCA), for understanding engineering development, physiology responses. A workshop was convened discuss purpose utility such an initiative, resulting in roadmap that acknowledges current knowledge gaps technical challenges, underscores how PCA initiative can help overcome them.

Language: Английский

Citations

65
Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives DOI Creative Commons

Xiaole Yu,

Zhixin Liu, Xuwu Sun

et al.

Plant Communications, Journal Year: 2022, Volume and Issue: 4(3), P. 100508 - 100508

Published: Dec. 20, 2022

Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial metabolomics techniques been combined to analyze development. These used study transcriptomes metabolomes tissues level, enabling systematic investigation gene expression metabolism specific during defined developmental stages. In this review, we present an overview significant breakthroughs multi-omics plants, discuss how these approaches may soon play essential roles research.

Language: Английский

Citations

61
Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume DOI Creative Commons
Sergio Alan Cervantes-Pérez,

Sandra Thibivilliers,

Carole Laffont

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(12), P. 1868 - 1888

Published: Nov. 1, 2022

Language: Английский

Citations

59
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data DOI
Manuel Neumann, Xiaocai Xu, Cezary Smaczniak

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 20, 2022

Language: Английский

Citations

54
Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits DOI Open Access

George Bawa,

Zhixin Liu,

Xiaole Yu

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(9), P. 4497 - 4497

Published: April 19, 2022

In recent years, advances in single-cell RNA sequencing (scRNA-seq) technologies have continued to change our views on biological systems by increasing the spatiotemporal resolution of analysis resolution. Application scRNA-seq plants enables comprehensive characterization both common and rare cell types states, uncovering new revealing how relate each other spatially developmentally. This review provides an overview methodologies, highlights application plant science, justifies why is a master player sequencing, explains role transcriptomics environmental stress adaptation, alongside challenges prospects transcriptomics. Collectively, we put forward central research.

Language: Английский

Citations

51