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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: 20 June 2024 | Viewed by 6503

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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

Published Papers (5 papers)

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Research

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 1 | Viewed by 710

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

Viewed by 982

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 - 03 Nov 2023

Viewed by 883

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 - 04 Sep 2023

Viewed by 1315

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 - 01 Jul 2023

Cited by 1 | Viewed by 1663

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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