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Latest Research on Plant Genomics and Genome Editing
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Latest Research on Plant Genomics and Genome Editing

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 4012

Special Issue Editor

Dr. Fabrizio Carbone

E-Mail Website
Guest Editor
Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
Interests: genomics; bioinformatics; plant biology; NBT; GWAS; olive breeding; photoperception; ripening; flowering; secondary metabolites

Special Issue Information

Dear Colleagues,

Scientists are able to edit genomes efficiently and cost-effectively thanks to the many high-quality reference genome sequences that are currently available. Zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system have been successfully employed to edit numerous individual genes in many organisms, and CRISPR-edited plants are now on the market. The CRISPR-Cas system has been widely used to edit genetic elements in genomes for various applications—not only crop improvement but also many gene therapy studies. In this Special Issue, we cordially invite scientists from around the world to contribute their cutting-edge research on plant genomics and genome editing. We welcome the submission of original research articles and short communications contributing to the advancement of genomics and genome editing, including techniques, applications, trait development, and enabling database and computational software. We are also inviting scientists to write reviews for this Special Issue.

Dr. Fabrizio Carbone
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next-generation sequencing
  • structural and functional genomics
  • SNPs
  • miRNA
  • LncRNA
  • CRISPR/Cas9
  • TALEN
  • genome editing

Published Papers (6 papers)

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Research

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15 pages, 3125 KiB  
Article
Unraveling a Small Secreted Peptide SUBPEP3 That Positively Regulates Salt-Stress Tolerance in Pyrus betulifolia
by Chaoran Xu, Ling Xiang, Wenting Huang, Xiao Zhang, Chong Mao, Shuang Wu, Tianzhong Li, Shengyuan Wang and Shengnan Wang
Int. J. Mol. Sci. 2024, 25(9), 4612; https://doi.org/10.3390/ijms25094612 - 23 Apr 2024
Viewed by 223
Abstract
Small secreted peptides (SSPs) play important roles in regulating plants’ growth and development in response to external stimulus, but the genes and functions of SSPs in many species are still unknown. Therefore, it is particularly significant to characterize and annotate SSP genes in [...] Read more.
Small secreted peptides (SSPs) play important roles in regulating plants’ growth and development in response to external stimulus, but the genes and functions of SSPs in many species are still unknown. Therefore, it is particularly significant to characterize and annotate SSP genes in plant genomes. As a widely used stock of pears, Pyrus betulifolia has strong resistance to biotic and abiotic stresses. In this study, we analyzed the SSPs genes in the genome of P. betulifolia according to their characteristics and homology. A total of 1195 SSP genes were identified, and most of them are signaling molecules. Among these, we identified a new SSP, subtilase peptide 3 (SUBPEP3), which derived from the PA region of preSUBPEP3, increasing the expression level under salt stress. Both adding synthetic peptide SUBPEP3 to the culture medium of pears and the overexpression of SUBPEP3 in tobacco can improve the salt tolerance of plants. In summary, we annotated the SSP genes in the P. betulifolia genome and identified a small secreted peptide SUBPEP3 that regulates the salt tolerance of P. betulifolia, which provides an important theoretical basis for further revealing the function of SSPs. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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16 pages, 3287 KiB  
Article
Systematic Analysis of DNA Demethylase Gene Families in Foxtail Millet (Setaria italica L.) and Their Expression Variations after Abiotic Stresses
by Yingying Sun, Xin Wang, Yunfei Di, Jinxiu Li, Keyu Li, Huanhuan Wei, Fan Zhang and Zhenxia Su
Int. J. Mol. Sci. 2024, 25(8), 4464; https://doi.org/10.3390/ijms25084464 - 18 Apr 2024
Viewed by 294
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. DNA demethylase (DNA-deMTase) genes have been identified in some plant species; however, there are no reports on the identification and analysis [...] Read more.
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. DNA demethylase (DNA-deMTase) genes have been identified in some plant species; however, there are no reports on the identification and analysis of DNA-deMTase genes in Foxtail millet (Setaria italica L.). In this study, seven DNA-deMTases were identified in S. italica. These DNA-deMTase genes were divided into four subfamilies (DML5, DML4, DML3, and ROS1) by phylogenetic and gene structure analysis. Further analysis shows that the physical and chemical properties of these DNA-deMTases proteins are similar, contain the typical conserved domains of ENCO3c and are located in the nucleus. Furthermore, multiple cis-acting elements were observed in DNA-deMTases, including light responsiveness, phytohormone responsiveness, stress responsiveness, and elements related to plant growth and development. The DNA-deMTase genes are expressed in all tissues detected with certain tissue specificity. Then, we investigated the abundance of DNA-deMTase transcripts under abiotic stresses (cold, drought, salt, ABA, and MeJA). The results showed that different genes of DNA-deMTases were involved in the regulation of different abiotic stresses. In total, our findings will provide a basis for the roles of DNA-deMTase in response to abiotic stress. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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17 pages, 4643 KiB  
Article
Genome-Wide Identification and Analysis of the EIN3/EIL Transcription Factor Gene Family in Doubled Haploid (DH) Poplar
by Caixia Liu, Erqin Fan, Yuhang Liu, Meng Wang, Qiuyu Wang, Sui Wang, Su Chen, Chuanping Yang, Xiangling You and Guanzheng Qu
Int. J. Mol. Sci. 2024, 25(7), 4116; https://doi.org/10.3390/ijms25074116 - 08 Apr 2024
Viewed by 469
Abstract
Ethylene (ET) is an important phytohormone that regulates plant growth, development and stress responses. The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor family, as a key regulator of the ET signal transduction pathway, plays an important role in regulating the expression of ET-responsive genes. Although studies [...] Read more.
Ethylene (ET) is an important phytohormone that regulates plant growth, development and stress responses. The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor family, as a key regulator of the ET signal transduction pathway, plays an important role in regulating the expression of ET-responsive genes. Although studies of EIN3/EIL family members have been completed in many species, their role in doubled haploid (DH) poplar derived from another culture of diploid Populus simonii × P. nigra (donor tree, DT) remains ambiguous. In this study, a total of seven EIN3/EIL gene family members in the DH poplar genome were identified. Basic physical and chemical property analyses of these genes were performed, and these proteins were predicted to be localized to the nucleus. According to the phylogenetic relationship, EIN3/EIL genes were divided into two groups, and the genes in the same group had a similar gene structure and conserved motifs. The expression patterns of EIN3/EIL genes in the apical buds of different DH poplar plants were analyzed based on transcriptome data. At the same time, the expression patterns of PsnEIL1, PsnEIN3, PsnEIL4 and PsnEIL5 genes in different tissues of different DH plants were detected via RT-qPCR, including the apical buds, young leaves, functional leaves, xylem, cambium and roots. The findings presented above indicate notable variations in the expression levels of PsnEIL genes across various tissues of distinct DH plants. Finally, the PsnEIL1 gene was overexpressed in DT, and the transgenic plants showed a dwarf phenotype, indicating that the PsnEIL1 gene was involved in regulating the growth and development of poplar. In this study, the EIN3/EIL gene family of DH poplar was analyzed and functionally characterized, which provides a theoretical basis for the future exploration of the EIN3/EIL gene function. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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15 pages, 3439 KiB  
Article
Genome-Wide Identification and Expression Profiling of Velvet Complex Transcription Factors in Populus alba × Populus glandulosa
by Yuanyuan Hao, Xiaojing Yan and Quanzi Li
Int. J. Mol. Sci. 2024, 25(7), 3926; https://doi.org/10.3390/ijms25073926 - 31 Mar 2024
Viewed by 578
Abstract
The discovery of new genes with novel functions is a major driver of adaptive evolutionary innovation in plants. Especially in woody plants, due to genome expansion, new genes evolve to regulate the processes of growth and development. In this study, we characterized the [...] Read more.
The discovery of new genes with novel functions is a major driver of adaptive evolutionary innovation in plants. Especially in woody plants, due to genome expansion, new genes evolve to regulate the processes of growth and development. In this study, we characterized the unique VeA transcription factor family in Populus alba × Populus glandulosa, which is associated with secondary metabolism. Twenty VeA genes were characterized systematically on their phylogeny, genomic distribution, gene structure and conserved motif, promoter binding site, and expression profiling. Furthermore, through ChIP-qPCR, Y1H, and effector-reporter assays, it was demonstrated that PagMYB128 directly regulated PagVeA3 to influence the biosynthesis of secondary metabolites. These results provide a basis for further elucidating the function of VeAs gene in poplar and its genetic regulation mechanism. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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24 pages, 4940 KiB  
Article
Whole-Transcriptome Profiling and Functional Prediction of Long Non-Coding RNAs Associated with Cold Tolerance in Japonica Rice Varieties
by Hao Wang, Yan Jia, Xu Bai, Weibin Gong, Ge Liu, Haixing Wang, Junying Xin, Yulong Wu, Hongliang Zheng, Hualong Liu, Jingguo Wang, Detang Zou and Hongwei Zhao
Int. J. Mol. Sci. 2024, 25(4), 2310; https://doi.org/10.3390/ijms25042310 - 15 Feb 2024
Viewed by 734
Abstract
Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures [...] Read more.
Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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Review

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38 pages, 13765 KiB  
Review
Not Only Editing: A Cas-Cade of CRISPR/Cas-Based Tools for Functional Genomics in Plants and Animals
by Aurélien Devillars, Gabriele Magon, Carlotta Pirrello, Fabio Palumbo, Silvia Farinati, Gianni Barcaccia, Margherita Lucchin and Alessandro Vannozzi
Int. J. Mol. Sci. 2024, 25(6), 3271; https://doi.org/10.3390/ijms25063271 - 13 Mar 2024
Viewed by 749
Abstract
The advent of CRISPR/Cas9 technology has revolutionized genome editing, enabling the attainment of once-unimaginable goals. CRISPR/Cas’s groundbreaking attributes lie in its simplicity, versatility, universality, and independence from customized DNA-protein systems, erasing the need for specialized expertise and broadening its scope of applications. It [...] Read more.
The advent of CRISPR/Cas9 technology has revolutionized genome editing, enabling the attainment of once-unimaginable goals. CRISPR/Cas’s groundbreaking attributes lie in its simplicity, versatility, universality, and independence from customized DNA-protein systems, erasing the need for specialized expertise and broadening its scope of applications. It is therefore more and more used for genome modification including the generation of mutants. Beyond such editing scopes, the recent development of novel or modified Cas-based systems has spawned an array of additional biotechnological tools, empowering both fundamental and applied research. Precisely targeting DNA or RNA sequences, the CRISPR/Cas system has been harnessed in fields as diverse as gene regulation, deepening insights into gene expression, epigenetic changes, genome spatial organization, and chromatin dynamics. Furthermore, it aids in genome imaging and sequencing, as well as effective identification and countering of viral pathogens in plants and animals. All in all, the non-editing aspect of CRISPR/Cas exhibits tremendous potential across diverse domains, including diagnostics, biotechnology, and fundamental research. This article reviews and critically evaluates the primary CRISPR/Cas-based tools developed for plants and animals, underlining their transformative impact. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing)
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