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

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants DOI Creative Commons
Rachel Shahan, Che‐Wei Hsu, Trevor M. Nolan

et al.

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(4), P. 543 - 560.e9

Published: Feb. 1, 2022

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal signatures underlying developmental trajectories. To map gene expression dynamics across root cell types time, we built a comprehensive, organ-scale atlas at single-cell resolution. addition to estimating progressions in pseudotime, employed mathematical concept of optimal transport infer trajectories identify their regulators. demonstrate utility interpret new datasets, profiled mutants two key regulators resolution, shortroot scarecrow. We report transcriptomic vivo evidence tissue trans-differentiation mixed identity phenotype Our results support as rich community resource unraveling programs that specify maintain regulate

Language: Английский

Citations

242
Cis-regulatory sequences in plants: Their importance, discovery, and future challenges DOI Creative Commons
Robert J. Schmitz, Erich Grotewold, Maike Stam

et al.

The Plant Cell, Journal Year: 2021, Volume and Issue: 34(2), P. 718 - 741

Published: Nov. 18, 2021

The identification and characterization of cis-regulatory DNA sequences how they function to coordinate responses developmental environmental cues is paramount importance plant biology. Key these regulatory processes are modules (CRMs), which include enhancers silencers. Despite the extraordinary advances in high-quality sequence assemblies genome annotations, understanding CRMs, regulate gene expression, lag significantly behind. This especially true for their distinguishing characteristics activity states. Here, we review current knowledge on CRMs breakthrough technologies enabling identification, characterization, validation CRMs; compare genomic distributions with respect target genes between different species, discuss role transposable elements harboring evolution expression. an exciting time study cis-regulomes plants; however, significant existing challenges need be overcome fully understand appreciate biology crop improvement.

Language: Английский

Citations

235
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research DOI Open Access
Carolin Seyfferth, Jim Renema, Jos R. Wendrich

et al.

Annual Review of Plant Biology, Journal Year: 2021, Volume and Issue: 72(1), P. 847 - 866

Published: March 17, 2021

Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of analyses to level individual cell. The field plant biology has fully embraced single-cell transcriptomics and is rapidly expanding portfolio available technologies applications. In this review, we give an overview main advances in over past few years provide reader with accessible guideline covering all steps, from sample preparation data analysis. We end offering a glimpse how these will shape accelerate plant-specific research near future.

Language: Английский

Citations

159
cis-Regulatory Elements in Plant Development, Adaptation, and Evolution DOI Creative Commons
Alexandre P. Marand, Andrea L. Eveland, Kerstin Kaufmann

et al.

Annual Review of Plant Biology, Journal Year: 2023, Volume and Issue: 74(1), P. 111 - 137

Published: Jan. 6, 2023

Regulatory elements encode the genomic blueprints that ensure proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to environment. Accumulating evidence implicates changes as a major source phenotypic novelty in eukaryotes, including acute phenotypes such disease cancer mammals. Moreover, genetic epigenetic variation affecting

Language: Английский

Citations

132
Epigenome plasticity in plants DOI
James P. B. Lloyd, Ryan Lister

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 23(1), P. 55 - 68

Published: Sept. 15, 2021

Language: Английский

Citations

124
Single-cell multi-omics in the medicinal plant Catharanthus roseus DOI Creative Commons
Chenxin Li, Joshua C. Wood, Anh Hai Vu

et al.

Nature Chemical Biology, Journal Year: 2023, Volume and Issue: 19(8), P. 1031 - 1041

Published: May 15, 2023

Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection transcripts and metabolites at level single cells high-resolution determination gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated monoterpene indole alkaloid (MIA) biosynthetic pathway Catharanthus roseus, source leading anticancer drugs. We identified clusters genes involved MIA biosynthesis on eight C. roseus chromosomes extensive duplication genes. Clustering was not limited to linear genome, through chromatin interaction data, were present within same topologically associated domain, permitting identification secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning leaf that, when coupled with single-cell metabolomics permitted reductase that yields bis-indole anhydrovinblastine. also expression root pathway.

Language: Английский

Citations

97
Single-cell technologies: From research to application DOI
Lu Wen, Guoqiang Li, Tao Huang

et al.

The Innovation, Journal Year: 2022, Volume and Issue: 3(6), P. 100342 - 100342

Published: Oct. 18, 2022

Language: Английский

Citations

88
Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root DOI
Trevor M. Nolan, Nemanja Vukašinović, Che‐Wei Hsu

et al.

Science, Journal Year: 2023, Volume and Issue: 379(6639)

Published: March 31, 2023

Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and elongation, through gene regulatory networks vary in space time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive expression specific different types developmental stages of the Arabidopsis root, we identified elongating cortex a site where brassinosteroids trigger shift from proliferation elongation associated with increased wall–related genes. Our analysis revealed HOMEOBOX FROM ARABIDOPSIS THALIANA 7 ( HAT7 ) GT-2-LIKE 1 GTL1 transcription factors elongation. These results establish brassinosteroid-mediated growth unveil brassinosteroid signaling network regulating transition which illuminates aspects spatiotemporal hormone responses.

Language: Английский

Citations

88
A pan-grass transcriptome reveals patterns of cellular divergence in crops DOI
Bruno Guillotin, Ramin Rahni, Michael J. Passalacqua

et al.

Nature, Journal Year: 2023, Volume and Issue: 617(7962), P. 785 - 791

Published: May 10, 2023

Language: Английский

Citations

87
Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis DOI Creative Commons
Lihua Zhang, Chao He, Yuting Lai

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 4, 2023

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.

Language: Английский

Citations

47