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Advances in Plant Genomics and Genome Editing
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Advances in Plant Genomics and Genome Editing

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 4083

Editor

Dr. Xuean Cui

E-Mail Website
Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: multiplex genome editing; multi-gene stacking; photosynthesis; leaf development; chloroplast development; crop genetics

Special Issue Information

Dear Colleagues,

Plant genome editing has revolutionized the improvement of crop, offering precise and efficient ways to enhance yield, resistance to pathogens, and nutritional value. Recent advances have enhanced the efficiency of editing, reduced off-target effects, and expanded the range of editable targets. These developments are crucial for addressing global challenges such as food security, climate change adaptation, and sustainable agriculture. This Special Issue, entitled "Advances in Plant Genomics and Genome Editing," explores cutting-edge developments in genome engineering tools and their applications in plant science. It highlights innovative strategies for trait improvement and discusses the ability of these technologies to address global challenges in food security and sustainable agriculture. The collection aims to provide researchers and breeders with insights into the latest genome editing techniques and their implications for crop improvement, including an understanding of the biological processes involved.

This Special Issue aims to showcase cutting-edge research on plant genome editing, focusing on CRISPR/Cas systems and advanced genome editing tools. We seek contributions that explore gene knock-out, knock-in, base editing, and prime editing techniques, as well as multiplex genome editing strategies. The Special Issue will highlight innovative genome editing tools, gene expression regulation, and their applications in the improvement of plant traits. Our aim is to provide a comprehensive overview of current advances in plant genome engineering, stimulating discussions on methodological improvements, novel applications, and the potential impact on crop enhancement.

In this Special Issue, original research articles and reviews are welcome. We welcome studies that push the boundaries of precision, efficiency, and versatility in plant genome modification.

I look forward to receiving your contributions.

Dr. Xuean Cui
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • plant genomes
  • plant genomics
  • genome sequencing
  • plant genome engineering
  • CRISPR/Cas
  • gene knock-out
  • gene knock-in
  • base editor
  • prime editor
  • genome editing tools
  • multiplex genome editing
  • gene expression regulation
  • plant trait improvement

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Published Papers (6 papers)

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Research

20 pages, 4061 KB  
Article
Genome-Wide Identification and Expression Analysis of the CesA/Csl Superfamily in Madhuca pasquieri
by Yule Chen, Jingzhe Qiu, Jiaxin Liu, Haoyou Lin, Lei Kan, Yihan Zheng, Jichen Wei and Lu Zhang
Biology 2026, 15(12), 895; https://doi.org/10.3390/biology15120895 - 6 Jun 2026
Viewed by 345
Abstract
The cellulose synthase gene superfamily encompasses two major groups, CesA and Csl, which are vital for synthesizing cellulose and hemicellulose in plant cell walls and fundamental to plant growth and developmental regulation. Madhuca pasquieri is a rare tree with high timber value. [...] Read more.
The cellulose synthase gene superfamily encompasses two major groups, CesA and Csl, which are vital for synthesizing cellulose and hemicellulose in plant cell walls and fundamental to plant growth and developmental regulation. Madhuca pasquieri is a rare tree with high timber value. Currently, there is no relevant report on the identification and characterization of the CesA/Csl gene family in M. pasquieri. In this study, based on the high-quality genome of M. pasquieri, 47 members of the CesA/Csl superfamily were identified and classified into seven subfamilies, including CesA, CslA, CslB, CslC, CslD, CslE and CslG. Cis-acting elements were identified via analysis of the 2000 bp upstream sequences of MpCesA, suggesting extensive involvement in biotic and abiotic stress regulation. Based on the transcriptome data of five growth periods, the expression of the CesA/Csl family was analyzed. Combined with phylogenetic information, it is inferred that MpCesA4/7b/7a/8b may regulate the secondary wall, while MpCesA1/3b/6b may regulate the primary wall. Protein–protein interaction showed that MpCesA4/7b/8a were in the core site. Finally, we constructed the cellulose synthase complex (MpCesA4/7b/8b) model using AlphaFold3, which suggests that MpCesA4/7b/8b may form a complex on the plasma membrane to carry out cellulose synthesis. This study has a limitation in that the complex and its expression lack experimental validation, and only data analysis is provided as a reference, offering some directions for future research. In summary, the systematic characterization of the MpCesA/Csl gene family provides important insights into cell wall formation, genetic enhancement, and future biotechnological applications of this species. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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15 pages, 10450 KB  
Article
Genome-Wide Identification and Expression Pattern Analysis of the GATA Gene Family Members in Scutellaria baicalensis Georgi Under Carbon Dot Treatment
by Qingbo Meng, Junbai Ma, Meitong Pan, Lingyang Kong, Qingdong Gao, Weichao Ren, Wei Ma and Xiubo Liu
Biology 2026, 15(11), 834; https://doi.org/10.3390/biology15110834 - 26 May 2026
Viewed by 251
Abstract
Scutellaria baicalensis Georgi is a crop with significant economic and medicinal value, but no studies have examined the GATA gene family in S. baicalensis or its expression patterns following foliar spray with nanomaterials. In this study, the GATA gene family in S. baicalensis [...] Read more.
Scutellaria baicalensis Georgi is a crop with significant economic and medicinal value, but no studies have examined the GATA gene family in S. baicalensis or its expression patterns following foliar spray with nanomaterials. In this study, the GATA gene family in S. baicalensis was identified and analyzed using bioinformatics. The results showed that 25 SbGATAs genes were identified, distributed across seven chromosomes, and could be classified into four subfamilies based on phylogenetic analysis. The physicochemical properties of SbGATAs proteins showed differences in the number of amino acids, molecular weight, and isoelectric point, but all were hydrophilic nuclear proteins. Analysis of cis-acting elements in the promoter regions revealed that the SbGATAs gene promoters were enriched for light, hormone response, and stress response elements. In this study, RT-qPCR was used to investigate the expression patterns of the SbGATAs family members in S. baicalensis leaves sprayed with different concentrations of carbon dot solutions. This study employed the RT-qPCR method to elucidate the expression of members of the SbGATAs family in the leaves of S. baicalensis after different treatments. The results showed that at low concentrations, except for SbGATA6, whose expression was upregulated by 2.1 times, the expressions of the other four genes were all downregulated; at high concentrations—except for SbGATA6, whose expression was upregulated by 3.75 times, and SbGATA14, the expression of which was basically the same as that of the control—the expressions of the other three genes were all downregulated. SbGATA6 was the only gene that was significantly upregulated at both concentrations and whose upregulation ratio increased with the increase in concentration, indicating that it may have a wide response to carbon dot treatment and may be involved in physiological regulation at different concentrations. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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17 pages, 2435 KB  
Article
Genome-Wide Identification and Expression Analysis of SS and SE Gene Families in Platycodon grandiflorum
by Meitong Pan, Junbai Ma, Denghua Wen, Lingyang Kong, Shan Jiang, Panpan Wang, Xiaozhuang Zhang, Weichao Ren, Wei Ma and Xiubo Liu
Biology 2026, 15(8), 620; https://doi.org/10.3390/biology15080620 - 16 Apr 2026
Viewed by 438
Abstract
At present, the characteristics of key enzyme genes in the upstream pathway for triterpenoid saponin biosynthesis in P. grandiflorum, as well as their expression patterns over the growth duration, have not been systematically analyzed. This study, at the whole-genome level, conducts the [...] Read more.
At present, the characteristics of key enzyme genes in the upstream pathway for triterpenoid saponin biosynthesis in P. grandiflorum, as well as their expression patterns over the growth duration, have not been systematically analyzed. This study, at the whole-genome level, conducts the first bioinformatics and expression analyses of the SS and SE gene families in P. grandiflorum. Four PgSS and seven PgSE genes were identified and distributed across six chromosomes. Members within the same subfamily exhibited highly conserved sequences and structures, while distinct structural divergence was observed between different subfamilies. Phylogenetic analysis showed that PgSS and PgSE genes were closely related to those of dicotyledons such as Panax ginseng and Polygala tenuifolia, suggesting high evolutionary conservation. Promoter analysis revealed abundant light- and hormone-responsive elements and MYB/MYC binding sites, indicating regulation by multiple signals. Protein secondary structures were dominated by the Alpha helix and were structurally stable. Quantitative real-time polymerase chain reaction (qPCR) demonstrated that expression levels of PgSS and PgSE in one-year-old Platycodonis Radix were significantly higher than in perennial Platycodonis Radix, especially for the PgSE family. This study characterized the basic biological features and growth-stage-dependent expression patterns of the SS and SE gene families in P. grandiflorum. The results identify key candidate genes and molecular targets for regulating triterpenoid saponin biosynthesis, and provide data supporting quality improvement and active metabolite research in this medicinal plant. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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19 pages, 10906 KB  
Article
Genome-Wide Identification and Expression Analysis of the HCT Gene Family in Upland Cotton (Gossypium hirsutum L.) in Response to Verticillium wilt Infection
by Yujia Zhang, Gang Liu, Baojun Liu, Mengxue Zhang, Yang Hu, Shu Wang, Jidi Sun and Aixing Gu
Biology 2026, 15(7), 520; https://doi.org/10.3390/biology15070520 - 25 Mar 2026
Viewed by 634
Abstract
Cotton, a globally vital cash crop, is severely constrained by V. dahliae. Lignin, a core structural component of plant cell walls, plays a crucial role in physical defense, with its biosynthesis regulated by hydroxycinnamoyltransferase (HCT)—a key enzyme in the phenylpropanoid pathway. However, [...] Read more.
Cotton, a globally vital cash crop, is severely constrained by V. dahliae. Lignin, a core structural component of plant cell walls, plays a crucial role in physical defense, with its biosynthesis regulated by hydroxycinnamoyltransferase (HCT)—a key enzyme in the phenylpropanoid pathway. However, the HCT gene family in upland cotton (Gossypium hirsutum) and its role in resistance to V. dahliae remain poorly understood. In this study, we performed a genome-wide identification of the HCT gene family in G. hirsutum, identifying 74 GhHCT genes that were classified into five evolutionary subfamilies. Bioinformatics analysis revealed that GhHCT proteins exhibit conserved functional domains but diverse gene structures, with promoter regions enriched in hormone-responsive and stress-responsive cis-acting elements. Expression profiling revealed that multiple GhHCT genes were significantly induced in response to V. dahliae infection. Three genes, GhHCT2, GhHCT35, and GhHCT47, showed significantly higher expression levels in resistant cultivars than in susceptible cultivars during early infection stages, suggesting pivotal roles in defense. These three candidate genes, which contain MeJA/SA-responsive elements in their promoters, may enhance resistance by regulating lignin synthesis to strengthen the cell wall barrier. In summary, this study provides the first comprehensive characterization of the HCT gene family in upland cotton. It identifies key candidates for improving resistance to V. dahliae, offering valuable genetic resources for molecular breeding. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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30 pages, 11130 KB  
Article
First Plastome Sequences of Two Endemic Taxa of Orbea Haw. from the Arabian Peninsula: Comparative Genomics and Phylogenetic Relationships Within the Tribe Ceropegieae (Asclepiadoideae, Apocynaceae)
by Samah A. Alharbi
Biology 2026, 15(3), 223; https://doi.org/10.3390/biology15030223 - 25 Jan 2026
Cited by 1 | Viewed by 756
Abstract
Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, [...] Read more.
Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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19 pages, 3726 KB  
Article
The Complete Mitochondrial Genome of Callicarpa americana L. Reveals the Structural Evolution and Size Differences in Lamiaceae
by Yang Wu, Jiayue Xu, Tenglong Hong, Jing He, Yuxiang Chen, Ye Zhang, Xinyu Hu, Huimin Sun, Li He and Dingkun Liu
Biology 2025, 14(12), 1747; https://doi.org/10.3390/biology14121747 - 5 Dec 2025
Viewed by 766
Abstract
Callicarpa americana L. is a member of the Lamiaceae family with important ornamental and medicinal value. Although the chloroplast genome of Lamiaceae has been extensively studied, its mitochondrial genome remains unreported, limiting a comprehensive understanding of the phylogeny and genome evolution of Lamiaceae. [...] Read more.
Callicarpa americana L. is a member of the Lamiaceae family with important ornamental and medicinal value. Although the chloroplast genome of Lamiaceae has been extensively studied, its mitochondrial genome remains unreported, limiting a comprehensive understanding of the phylogeny and genome evolution of Lamiaceae. In this study, the complete mitochondrial genome of C. americana was successfully assembled for the first time. The genome is 499,565 bp in length, showing a complex multi-branched closed-loop structure that contains 37 protein-coding genes, 23 tRNA genes, and 4 rRNA genes. The difference in mitochondrial genome size is relatively large compared to Orobanchaceae species, but the difference in GC content is not obvious. The expansion of genome size was mainly due to the accumulation of non-coding regions and repetitive sequences. Meanwhile, two pairs of long repetitive sequences (LR3 and LR5) mediated homologous recombination. The mitogenome was also identified; there were a total of 494 C-to-U RNA editing sites in protein-coding genes. In addition, 42 mitochondrial plastid DNA fragments (MTPTs) were detected, with a total length of 21,464 bp, accounting for 4.30% of the genome. Repeat sequence analysis showed that tetranucleotide SSR was the most abundant repeat type in the mitochondria of Lamiaceae. Phylogenetic analysis based on the alignment of 32 protein-coding gene sequences showed that Callicarpa is sister to the other eight species of Lamiaceae. This work fills an important gap by presenting the first complete mitochondrial genome of C. americana, providing an important data resource for further understanding the structural evolution, dynamic recombination mechanism, and phylogeny of the mitochondrial genome of Lamiaceae. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)
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