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Advances in the Identification and Characterization of Plant Genes

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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: closed (20 June 2024) | Viewed by 11460

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Dr. Frank M. You

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Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
Interests: plant bioinformatics; comparative genomics; genome evolution; quantitative genetics and statistical genomics; genetics and breeding; software tool and database development
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Dear Colleagues,

We are pleased to announce a Special Issue on ‘Advances in the Identification and Characterization of Plant Genes’ that will be published in the International Journal of Molecular Sciences. This Special Issue aims to provide a comprehensive overview of the latest research in the field of plant gene identification and characterization.

Plant genomes are incredibly complex, and identifying and characterizing individual genes within them is a significant challenge. However, advances in sequencing technologies and bioinformatics tools have made it possible to overcome many of these challenges and enhance our understanding of plant genomics.

This Special Issue will address a wide range of topics related to plant gene identification and characterization, including genome sequencing and annotation, transcriptomics, proteomics, and functional analysis. We welcome original research articles, reviews, and perspectives that address these topics and provide new insights into the molecular mechanisms that underlie plant growth, development, and responses to biotic and abiotic stress.

We encourage submissions from researchers across the globe who are currently employed in plant genomics and welcome contributions that reflect both fundamental and applied research. Our aim is to assemble cutting-edge research that will promote advancements in our understanding of plant gene regulation and pave the way for the development of new and improved crops.

We look forward to receiving your submissions and to sharing this exciting collection of research with our readers.

Dr. Frank M. You
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

gene identification
gene characterization
functional genomics
sequencing technologies
bioinformatics tools
plant genomics
genome sequencing
transcriptomics
proteomics
functional analysis
biotic stress
abiotic stress
quantitative trait loci
genome-wide association study
gene expression
gene regulation

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Published Papers (7 papers)

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Research

20 pages, 12432 KiB

Open AccessArticle

Divergent Roles of the Auxin Response Factors in Lemongrass (Cymbopogon flexuosus (Nees ex Steud.) W. Watson) during Plant Growth

by Guoli Wang, Jian Zeng, Canghao Du, Qi Tang, Yuqing Hua, Mingjie Chen, Guangxiao Yang, Min Tu, Guangyuan He, Yin Li, Jinming He and Junli Chang

Int. J. Mol. Sci. 2024, 25(15), 8154; https://doi.org/10.3390/ijms25158154 - 26 Jul 2024

Cited by 1 | Viewed by 731

Abstract

Auxin Response Factors (ARFs) make up a plant-specific transcription factor family that mainly couples perception of the phytohormone, auxin, and gene expression programs and plays an important and multi-faceted role during plant growth and development. Lemongrass (Cymbopogon flexuosus) is a representative Cymbopogon species widely used in gardening, beverages, fragrances, traditional medicine, and heavy metal phytoremediation. Biomass yield is an important trait for several agro-economic purposes of lemongrass, such as landscaping, essential oil production, and phytoremediation. Therefore, we performed gene mining of CfARFs and identified 26 and 27 CfARF-encoding genes in each of the haplotype genomes of lemongrass, respectively. Phylogenetic and domain architecture analyses showed that CfARFs can be divided into four groups, among which groups 1, 2, and 3 correspond to activator, repressor, and ETTN-like ARFs, respectively. To identify the CfARFs that may play major roles during the growth of lemongrass plants, RNA-seq was performed on three tissues (leaf, stem, and root) and four developmental stages (3-leaf, 4-leaf, 5-leaf. and mature stages). The expression profiling of CfARFs identified several highly expressed activator and repressor CfARFs and three CfARFs (CfARF3, 18, and 35) with gradually increased levels during leaf growth. Haplotype-resolved transcriptome analysis revealed that biallelic expression dominance is frequent among CfARFs and contributes to their gene expression patterns. In addition, co-expression network analysis identified the modules enriched with CfARFs. By establishing orthologous relationships among CfARFs, sorghum ARFs, and maize ARFs, we showed that CfARFs were mainly expanded by whole-genome duplications, and that the duplicated CfARFs might have been divergent due to differential expression and variations in domains and motifs. Our work provides a detailed catalog of CfARFs in lemongrass, representing a first step toward characterizing CfARF functions, and may be useful in molecular breeding to enhance lemongrass plant growth. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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19 pages, 8226 KiB

Open AccessArticle

Genome-Wide Analysis of the WOX Family and Its Expression Pattern in Root Development of Paeonia ostii

by Xueyuan Lou, Jiange Wang, Guiqing Wang, Dan He, Wenqian Shang, Yinglong Song, Zheng Wang and Songlin He

Int. J. Mol. Sci. 2024, 25(14), 7668; https://doi.org/10.3390/ijms25147668 - 12 Jul 2024

Viewed by 797

Abstract

Tree peony (Paeonia suffruticosa Andr.) is a woody plant with high ornamental, medicinal, and oil values. However, its low rooting rate and poor rooting quality are bottleneck issues in the micropropagation of P. ostii. The WUSCHEL-related homeobox (WOX) family plays a crucial role in root development. In this study, based on the screening of the genome and root transcriptome database, we identified ten WOX members in P. ostii. Phylogenetic analysis revealed that the ten PoWOX proteins clustered into three major clades, the WUS, intermediate, and ancient clade, respectively. The conserved motifs and tertiary structures of PoWOX proteins located in the same clade exhibited higher similarity. The analysis of cis-regulatory elements in the promoter indicated that PoWOX genes are involved in plant growth and development, phytohormones, and stress responses. The expression analysis revealed that PoWOX genes are expressed in distinct tissues. PoWOX4, PoWOX5, PoWOX11, and PoWOX13b are preferentially expressed in roots at the early stage of root primordium formation, suggesting their role in the initiation and development of roots. These results will provide a comprehensive reference for the evolution and potential function of the WOX family and offer guidance for further study on the root development of tree peony. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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23 pages, 6043 KiB

Open AccessArticle

GhCNGC13 and 32 Act as Critical Links between Growth and Immunity in Cotton

by Song Peng, Panyu Li, Tianming Li, Zengyuan Tian and Ruqiang Xu

Int. J. Mol. Sci. 2024, 25(1), 1; https://doi.org/10.3390/ijms25010001 - 19 Dec 2023

Cited by 2 | Viewed by 1198

Abstract

Cyclic nucleotide-gated ion channels (CNGCs) remain poorly studied in crop plants, most of which are polyploid. In allotetraploid Upland cotton (Gossypium hirsutum), silencing GhCNGC13 and 32 impaired plant growth and shoot apical meristem (SAM) development, while triggering plant autoimmunity. Both growth hormones (indole-3-acetic acid and gibberellin) and stress hormones (abscisic acid, salicylic acid, and jasmonate) increased, while leaf photosynthesis decreased. The silenced plants exhibited an enhanced resistance to Botrytis cinerea; however, Verticillium wilt resistance was weakened, which was associated with LIPOXYGENASE2 (LOX2) downregulation. Transcriptomic analysis of silenced plants revealed 4835 differentially expressed genes (DEGs) with functional enrichment in immunity and photosynthesis. These DEGs included a set of transcription factors with significant over-representation in the HSF, NAC, and WRKY families. Moreover, numerous members of the GhCNGC family were identified among the DEGs, which may indicate a coordinated action. Collectively, our results suggested that GhCNGC13 and 32 functionally link to photosynthesis, plant growth, and plant immunity. We proposed that GhCNGC13 and 32 play a critical role in the “growth–defense tradeoff” widely observed in crops. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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26 pages, 19811 KiB

Open AccessArticle

Yellow-Green Leaf 19 Encoding a Specific and Conservative Protein for Photosynthetic Organisms Affects Tetrapyrrole Biosynthesis, Photosynthesis, and Reactive Oxygen Species Metabolism in Rice

by Qiang Wang, Hongyu Zhang, Lingxia Wei, Rong Guo, Xuanzhi Liu, Miao Zhang, Jiangmin Fan, Siyi Liu, Jianglin Liao, Yingjin Huang and Zhaohai Wang

Int. J. Mol. Sci. 2023, 24(23), 16762; https://doi.org/10.3390/ijms242316762 - 25 Nov 2023

Cited by 1 | Viewed by 1580

Abstract

Chlorophyll is the main photosynthetic pigment and is crucial for plant photosynthesis. Leaf color mutants are widely used to identify genes involved in the synthesis or metabolism of chlorophyll. In this study, a spontaneous mutant, yellow-green leaf 19 (ygl19), was isolated from rice (Oryza sativa). This ygl19 mutant showed yellow-green leaves and decreased chlorophyll level and net photosynthetic rate. Brown necrotic spots appeared on the surface of ygl19 leaves at the tillering stage. And the agronomic traits of the ygl19 mutant, including the plant height, tiller number per plant, and total number of grains per plant, were significantly reduced. Map-based cloning revealed that the candidate YGL19 gene was LOC_Os03g21370. Complementation of the ygl19 mutant with the wild-type CDS of LOC_Os03g21370 led to the restoration of the mutant to the normal phenotype. Evolutionary analysis revealed that YGL19 protein and its homologues were unique for photoautotrophs, containing a conserved Ycf54 functional domain. A conserved amino acid substitution from proline to serine on the Ycf54 domain led to the ygl19 mutation. Sequence analysis of the YGL19 gene in 4726 rice accessions found that the YGL19 gene was conserved in natural rice variants with no resulting amino acid variation. The YGL19 gene was mainly expressed in green tissues, especially in leaf organs. And the YGL19 protein was localized in the chloroplast for function. Gene expression analysis via qRT-PCR showed that the expression levels of tetrapyrrole synthesis-related genes and photosynthesis-related genes were regulated in the ygl19 mutant. Reactive oxygen species (ROS) such as superoxide anions and hydrogen peroxide accumulated in spotted leaves of the ygl19 mutant at the tillering stage, accompanied by the regulation of ROS scavenging enzyme-encoding genes and ROS-responsive defense signaling genes. This study demonstrates that a novel yellow-green leaf gene YGL19 affects tetrapyrrole biosynthesis, photosynthesis, and ROS metabolism in rice. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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16 pages, 20840 KiB

Open AccessArticle

Genome-Wide Analysis of bHLH Family Genes and Identification of Members Associated with Cold/Drought-Induced Photoinhibition in Kandelia obovata

by Junjian Li, Siyi Chen, Yaxin Yin, Qiaobo Shan, Chunfang Zheng and Yan Chen

Int. J. Mol. Sci. 2023, 24(21), 15942; https://doi.org/10.3390/ijms242115942 - 3 Nov 2023

Cited by 1 | Viewed by 1398

Abstract

Plant basic helix-loop-helix (bHLH) transcription factors play pivotal roles in responding to stress, including cold and drought. However, it remains unclear how bHLH family genes respond to these stresses in Kandelia obovata. In this study, we identified 75 bHLH members in K. obovata, classified into 11 subfamilies and unevenly distributed across its 18 chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of KobHLH genes. The KobHLH promoters were enriched with elements associated with light response. Through RNA-seq, we identified several cold/drought-associated KobHLH genes. This correlated with decreased net photosynthetic rates (P_n) in the leaves of cold/drought-treated plants. Weighted gene co-expression network analysis (WGCNA) confirmed that 11 KobHLH genes were closely linked to photoinhibition in photosystem II (PS II). Among them, four Phytochrome Interacting Factors (PIFs) involved in chlorophyll metabolism were significantly down-regulated. Subcellular localization showed that KobHLH52 and KobHLH30 were located in the nucleus. Overall, we have comprehensively analyzed the KobHLH family and identified several members associated with photoinhibition under cold or drought stress, which may be helpfulfor further cold/drought-tolerance enhancement and molecular breeding through genetic engineering in K. obovata. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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15 pages, 3403 KiB

Open AccessArticle

Genome-Wide Analysis of SPL/miR156 Module and Its Expression Analysis in Vegetative and Reproductive Organs of Oil Palm (Elaeis guineensis)

by Lixia Zhou and Rajesh Yarra

Int. J. Mol. Sci. 2023, 24(17), 13658; https://doi.org/10.3390/ijms241713658 - 4 Sep 2023

Cited by 2 | Viewed by 1799

Abstract

The SPL (SQUAMOSA-promoter binding protein-like) gene family is one of the largest plant transcription factors and is known to be involved in the regulation of plant growth, development, and stress responses. The genome-wide analysis of SPL gene members in a diverse range of crops has been elucidated. However, none of the genome-wide studies on the SPL gene family have been carried out for oil palm, an important oil-yielding plant. In this research, a total of 24 EgSPL genes were identified via a genome-wide approach. Phylogenetic analysis revealed that most of the EgSPLs are closely related to the Arabidopsis and rice SPL gene members. EgSPL genes were mapped onto the only nine chromosomes of the oil palm genome. Motif analysis revealed conservation of the SBP domain and the occurrence of 1–10 motifs in EgSPL gene members. Gene duplication analysis demonstrated the tandem duplication of SPL members in the oil palm genome. Heatmap analysis indicated the significant expression of SPL genes in shoot and flower organs of oil palm plants. Among the identified EgSPL genes, a total 14 EgSPLs were shown to be targets of miR156. Real-time PCR analysis of 14 SPL genes showed that most of the EgSPL genes were more highly expressed in female and male inflorescences of oil palm plants than in vegetative tissues. Altogether, the present study revealed the significant role of EgSPL genes in inflorescence development. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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23 pages, 9957 KiB

Open AccessArticle

Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation

by Jiaqi Chen, Yushuang Yang, Chuang Li, Qiuhui Chen, Shizhong Liu and Bi Qin

Int. J. Mol. Sci. 2023, 24(13), 10997; https://doi.org/10.3390/ijms241310997 - 1 Jul 2023

Cited by 3 | Viewed by 2487

Abstract

MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS. Full article

(This article belongs to the Special Issue Advances in the Identification and Characterization of Plant Genes)

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