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Applied and Advanced Research in Plant Bioinformatics

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

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 17873

Special Issue Editors


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Guest Editor
Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Korea
Interests: next generation sequencing; genomics; proteomics; evolutionary developmental genetics; plant molecular interaction

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Co-Guest Editor
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju-55365, Korea
Interests: Plant genomics; Secondary metabolites; Proteomics; LEDs; Molecular markers; Medicinal plants; NGS in plant breeding
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Special Issue Information

Dear Colleagues,

Advances in Bioinformatics has revolutionized the conventional way of handling data in life science with established analytic tools. High-throughput computational techniques unambiguously resolve the bottlenecks in several biological concerns. Understanding of protein structural interactions by modeling, docking, and molecular simulations have become essential to address biologically important processes. In the crop improvement area of research, bioinformatics studies on functional annotation of gene, genome architecture, chromosomal cross-over, re-shuffling of chromosomal region have facilitated the understanding of  comparative evolutionary and domestication process. Identification and characterization of gene(s) responsible for particular trait of interest is necessary for forward and reverse genetics in crop science. The present era of next generation sequencing (NGS) brings genome-scale resolution on organism and complex molecular mechanisms. Processing big data on whole genome sequencing and re-sequencing, discovery of molecular markers  from large set of population are vital for genome assisted selection (GAS). Consequently, recent genome editing generates genetic variability in plants with utmost efficiency. Considering the importance and in evitable necessity of computational biology, particularly for the development of novel varieties in agricultural and horticultural crops, we are elated to host a holistic compilation of researches and reviews focusing on the application of bioinformatics in plant biology.

For this special issue we welcome the manuscripts dealing with applied and advanced researches in plant bioinformatics. Tools, softwares, and database developed in related to plant science are also encouraged to submit. Manuscripts related to following but not limited to considered for this special issue.

Dr. Prabhakaran Soundararajan
Dr. Abinaya Manivannan
Guest Editors

Manuscript Submission Information

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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

  • Protein modeling
  • Macromolecular Docking
  • Molecular simulation
  • Gene characterization
  • Genome assembly and annotation
  • Comparative genomics
  • Evolutionary analysis
  • Re-sequencing
  • Genome Editing

Published Papers (7 papers)

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Research

11 pages, 12909 KiB  
Article
cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments
by Mingeun Ji, Yejin Kan, Dongyeon Kim, Jaehee Jung and Gangman Yi
Int. J. Mol. Sci. 2022, 23(19), 11484; https://doi.org/10.3390/ijms231911484 - 29 Sep 2022
Cited by 1 | Viewed by 1413
Abstract
Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, [...] Read more.
Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, it is essential to analyze the results of read alignments for a biologically meaningful inference. However, read alignment from vast amounts of genomic data from various organisms is challenging in that it involves repeated automatic and manual analysis steps. We, here, devised cPlot software for read alignment of nucleotide sequences, with automated read alignment and position analysis, which allows visual assessment of the analysis results by the user. cPlot compares sequence similarity of reads by performing multiple read alignments, with FASTA format files as the input. This application provides a web-based interface for the user for facile implementation, without the need for a dedicated computing environment. cPlot identifies the location and order of the sequencing reads by comparing the sequence to a genetically close reference sequence in a way that is effective for visualizing the assembly of short reads generated by NGS and rapid gene map construction. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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19 pages, 5869 KiB  
Article
Genome-Wide Identification and Expression of MAPK Gene Family in Cultivated Strawberry and Their Involvement in Fruit Developing and Ripening
by Mengyao Li, Binghua Li, Min Yang, Liangxin Wang, Guoyan Hou, Yuanxiu Lin, Yunting Zhang, Yong Zhang, Qing Chen, Yan Wang, Wen He, Xiaorong Wang, Haoru Tang, Guichuan Yang and Ya Luo
Int. J. Mol. Sci. 2022, 23(9), 5201; https://doi.org/10.3390/ijms23095201 - 6 May 2022
Cited by 11 | Viewed by 2420
Abstract
Studies on many plants have shown that mitogen-activated protein kinases (MAPKs) are key proteins involved in regulating plant responses to biotic and abiotic stresses. However, their involvement in cultivated strawberry development and ripening remains unclear. In this study, 43 FaMAPK gene family members [...] Read more.
Studies on many plants have shown that mitogen-activated protein kinases (MAPKs) are key proteins involved in regulating plant responses to biotic and abiotic stresses. However, their involvement in cultivated strawberry development and ripening remains unclear. In this study, 43 FaMAPK gene family members were identified in the genome of cultivated strawberry (Fragaria × ananassa), phylogenetic analysis indicated that FaMAPKs could be classified into four groups. Systematic analysis of the conserved motif, exon–intron structure showed that there were significant varieties between different groups in structure, but in the same group they were similar. Multiple cis-regulatory elements associated with phytohormone response, and abiotic and biotic stresses were predicted in the promoter regions of FaMAPK genes. Transcriptional analysis showed that all FaMAPK genes were expressed at all developmental stages. Meanwhile, the effect of exogenous ABA and sucrose on the expression profile of FaMAPKs was investigated. Exogenous ABA, sucrose, and ABA plus sucrose treatments upregulated the expression of FaMAPK genes and increased the content of endogenous ABA, sucrose, and anthocyanin in strawberry fruits, suggesting that ABA and sucrose might be involved in the FaMAPK-mediated regulation of strawberry fruit ripening. Based on the obtained results, MAPK genes closely related to the ripening of strawberries were screened to provide a theoretical basis and support for future research on strawberries. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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21 pages, 7385 KiB  
Article
Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
by Yuting Xie, Yeting Gu, Guangping Shi, Jianliang He, Wenjing Hu and Zhonghui Zhang
Int. J. Mol. Sci. 2022, 23(5), 2680; https://doi.org/10.3390/ijms23052680 - 28 Feb 2022
Cited by 8 | Viewed by 2692
Abstract
Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide [...] Read more.
Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and biological function of plant PUSs. In this study, we identified 20 AtPUSs and 22 ZmPUSs from Arabidopsis and maize (Zea mays), respectively. Our phylogenetic analysis indicated that both AtPUSs and ZmPUSs could be clustered into six known subfamilies: RluA, RsuA, TruA, TruB, PUS10, and TruD. RluA subfamily is the largest subfamily in both Arabidopsis and maize. It’s noteworthy that except the canonical XXHRLD-type RluAs, another three conserved RluA variants, including XXNRLD-, XXHQID-, and XXHRLG-type were also identified in those key nodes of vascular plants. Subcellular localization analysis of representative AtPUSs and ZmPUSs in each subfamily revealed that PUS proteins were localized in different organelles including nucleus, cytoplasm and chloroplasts. Transcriptional expression analysis indicated that AtPUSs and ZmPUSs were differentially expressed in various tissues and diversely responsive to abiotic stresses, especially suggesting their potential roles in response to heat and salt stresses. All these results would facilitate the functional identification of these pseudouridylation in the future. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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20 pages, 4616 KiB  
Article
Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
by Carlos Peña-Varas, Christa Kanstrup, Ariela Vergara-Jaque, Mariela González-Avendaño, Christoph Crocoll, Osman Mirza, Ingo Dreyer, Hussam Nour-Eldin and David Ramírez
Int. J. Mol. Sci. 2022, 23(3), 1595; https://doi.org/10.3390/ijms23031595 - 29 Jan 2022
Cited by 4 | Viewed by 2441
Abstract
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis [...] Read more.
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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26 pages, 5377 KiB  
Article
Two Novel Dimorphism-Related Virulence Factors of Zymoseptoria tritici Identified Using Agrobacterium-Mediated Insertional Mutagenesis
by Alexander Yemelin, Annamaria Brauchler, Stefan Jacob, Andrew J. Foster, Julian Laufer, Larissa Heck, Luis Antelo, Karsten Andresen and Eckhard Thines
Int. J. Mol. Sci. 2022, 23(1), 400; https://doi.org/10.3390/ijms23010400 - 30 Dec 2021
Cited by 4 | Viewed by 2330
Abstract
Diseases caused by dimorphic phytopathogenic and systemic dimorphic fungi have markedly increased in prevalence in the last decades, and understanding the morphogenic transition to the virulent state might yield novel means of controlling dimorphic fungi. The dimorphic fungus Z. tritici causes significant economic [...] Read more.
Diseases caused by dimorphic phytopathogenic and systemic dimorphic fungi have markedly increased in prevalence in the last decades, and understanding the morphogenic transition to the virulent state might yield novel means of controlling dimorphic fungi. The dimorphic fungus Z. tritici causes significant economic impact on wheat production, and yet the regulation of the dimorphic switch, a key first step in successful plant colonization, is still largely unexplored in this fungus. The fungus is amenable to suppression by fungicides at this switch point, and the identification of the factors controlling the dimorphic switch provides a potential source of novel targets to control Septoria tritici blotch (STB). Inhibition of the dimorphic switch can potentially prevent penetration and avoid any damage to the host plant. The aim of the current work was to unveil genetic determinants of the dimorphic transition in Z. tritici by using a forward genetics strategy. Using this approach, we unveiled two novel factors involved in the switch to the pathogenic state and used reverse genetics and complementation to confirm the role of the novel virulence factors and further gained insight into the role of these genes, using transcriptome analysis via RNA-Seq. The transcriptomes generated potentially contain key determinants of the dimorphic transition. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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22 pages, 8862 KiB  
Article
Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus
by Shuo Han, Zhiyin Jiao, Meng-Xue Niu, Xiao Yu, Mengbo Huang, Chao Liu, Hou-Ling Wang, Yangyan Zhou, Wei Mao, Xiaofei Wang, Weilun Yin and Xinli Xia
Int. J. Mol. Sci. 2021, 22(22), 12336; https://doi.org/10.3390/ijms222212336 - 15 Nov 2021
Cited by 22 | Viewed by 2926
Abstract
Gibberellic acid-stimulated Arabidopsis (GASA) proteins, as cysteine-rich peptides (CRPs), play roles in development and reproduction and biotic and abiotic stresses. Although the GASA gene family has been identified in plants, the knowledge about GASAs in Populus euphratica, the woody model plant for [...] Read more.
Gibberellic acid-stimulated Arabidopsis (GASA) proteins, as cysteine-rich peptides (CRPs), play roles in development and reproduction and biotic and abiotic stresses. Although the GASA gene family has been identified in plants, the knowledge about GASAs in Populus euphratica, the woody model plant for studying abiotic stress, remains limited. Here, we referenced the well-sequenced Populus trichocarpa genome, and identified the GASAs in the whole genome of P. euphratica and P. trichocarpa. 21 candidate genes in P. trichocarpa and 19 candidate genes in P. euphratica were identified and categorized into three subfamilies by phylogenetic analysis. Most GASAs with signal peptides were located extracellularly. The GASA genes in Populus have experienced multiple gene duplication events, especially in the subfamily A. The evolution of the subfamily A, with the largest number of members, can be attributed to whole-genome duplication (WGD) and tandem duplication (TD). Collinearity analysis showed that WGD genes played a leading role in the evolution of GASA genes subfamily B. The expression patterns of P. trichocarpa and P. euphratica were investigated using the PlantGenIE database and the real-time quantitative PCR (qRT-PCR), respectively. GASA genes in P. trichocarpa and P. euphratica were mainly expressed in young tissues and organs, and almost rarely expressed in mature leaves. GASA genes in P. euphratica leaves were also widely involved in hormone responses and drought stress responses. GUS activity assay showed that PeuGASA15 was widely present in various organs of the plant, especially in vascular bundles, and was induced by auxin and inhibited by mannitol dramatically. In summary, this present study provides a theoretical foundation for further research on the function of GASA genes in P. euphratica. Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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12 pages, 1597 KiB  
Article
GreeningDB: A Database of Host–Pathogen Protein–Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease
by Cristian D. Loaiza, Naveen Duhan and Rakesh Kaundal
Int. J. Mol. Sci. 2021, 22(19), 10897; https://doi.org/10.3390/ijms221910897 - 8 Oct 2021
Cited by 3 | Viewed by 2481
Abstract
The Citrus genus comprises some of the most important and commonly cultivated fruit plants. Within the last decade, citrus greening disease (also known as huanglongbing or HLB) has emerged as the biggest threat for the citrus industry. This disease does not have a [...] Read more.
The Citrus genus comprises some of the most important and commonly cultivated fruit plants. Within the last decade, citrus greening disease (also known as huanglongbing or HLB) has emerged as the biggest threat for the citrus industry. This disease does not have a cure yet and, thus, many efforts have been made to find a solution to this devastating condition. There are challenges in the generation of high-yield resistant cultivars, in part due to the limited and sparse knowledge about the mechanisms that are used by the Liberibacter bacteria to proliferate the infection in Citrus plants. Here, we present GreeningDB, a database implemented to provide the annotation of Liberibacter proteomes, as well as the host–pathogen comparactomics tool, a novel platform to compare the predicted interactomes of two HLB host–pathogen systems. GreeningDB is built to deliver a user-friendly interface, including network visualization and links to other resources. We hope that by providing these characteristics, GreeningDB can become a central resource to retrieve HLB-related protein annotations, and thus, aid the community that is pursuing the development of molecular-based strategies to mitigate this disease’s impact. The database is freely available at http://bioinfo.usu.edu/GreeningDB/ (accessed on 11 August 2021). Full article
(This article belongs to the Special Issue Applied and Advanced Research in Plant Bioinformatics)
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