Development and prospect of gene-edited fruits and vegetables

Zhang, Siyuan; Zhu, Hongliang

doi:10.1093/fqsafe/fyad045

Cited by 4 publications

(1 citation statement)

References 113 publications

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“…Genome editing is widely performed in various organisms [1–4]. This technology harnesses programmable nucleases including zinc finger nucleases (ZFNs) [5, 6], transcription activator-like effector nucleases (TALENs) [7], and clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) [8–10].…”

Section: Introductionmentioning

confidence: 99%

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

Nakamae,

Ide,

Ohnuki

et al. 2024

Preprint

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Background: Tracking of Insertions and DEletions (TIDE) analysis, which computationally deconvolves capillary sequencing data derived from the DNA of bulk or clonal cell populations to estimate the efficiency of targeted mutagenesis by programmable nucleases, has played a significant role in the field of genome editing. However, the detection range covered by conventional TIDE analysis is limited. Range extension for deconvolution is required to detect larger deletions and insertions (indels) derived from genome editing in TIDE analysis. However, extending the deconvolution range introduces uncertainty into the deconvolution process. Moreover, the accuracy and sensitivity of TIDE analysis tools for large deletions (>50 bp) remain poorly understood. Results: In this study, we introduced a new software called PtWAVE that can detect a wide range of indel sizes, up to 200 bp. PtWAVE also offers options for variable selection and fitting algorithms to prevent uncertainties in the model. We evaluated the performance of PtWAVE by using in vitro capillary sequencing data that mimicked DNA sequencing, including large deletions. Furthermore, we confirmed that PtWAVE can stably analyze trace sequencing data derived from actual genome-edited samples. Conclusions: PtWAVE demonstrated superior accuracy and sensitivity compared to the existing TIDE analysis tools for DNA samples, including large deletions. PtWAVE can accelerate genome editing applications in organisms and cell types in which large deletions often occur when programmable nucleases are applied.

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Section: Introductionmentioning

confidence: 99%

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

Nakamae,

Ide,

Ohnuki

et al. 2024

Preprint

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Enhancing nutritional quality in vegetables through breeding and cultivar choice in protected cultivation

Weiss,

Gruda

2025

Scientia Horticulturae

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WRKY Transcription Factors (TFs) as Key Regulators of Plant Resilience to Environmental Stresses: Current Perspective

Li,

Khoso,

et al. 2024

Agronomy

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Plants encounter various stresses in their natural environments and can effectively respond to only one stress at a time. Through a complex gene network, transcription factors (TFs) such as WRKY TFs regulate a diverse array of stress responses. The clarification of the structural characteristics of WRKY proteins, along with recent advancements in molecular dynamics simulations, has shed light on the formation, stability, and interactions of DNA–protein complexes. This has provided a novel viewpoint regarding the control of WRKY TFs. The investigation of superfamilies, encompassing their historical development, diversity, and evolutionary patterns, has become feasible due to the transcriptome approach’s capacity to provide extensive and comprehensive transcripts. The significance of WRKY TFs lies in their pivotal role within several signaling cascades and regulatory networks that influence plant defense responses. The present review summarizes the functional aspects of the high-volume sequence data of WRKY TFs from different species studied to date. Moreover, a comparative analysis approach was utilized to determine the functions of the identified WRKY TFs in response to both abiotic and biotic stresses, as revealed through numerous studies on different plant species. The results of this review will be pivotal in understanding evolutionary events and the significance of WRKY TFs in the context of climate change, incorporating new scientific evidence to propose an innovative viewpoint.

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Development and prospect of gene-edited fruits and vegetables

Cited by 4 publications

References 113 publications

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

Enhancing nutritional quality in vegetables through breeding and cultivar choice in protected cultivation

WRKY Transcription Factors (TFs) as Key Regulators of Plant Resilience to Environmental Stresses: Current Perspective

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