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Application of Bioinformatics in Plants
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Application of Bioinformatics in Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (20 June 2023) | Viewed by 9208

Special Issue Editor

Prof. Dr. Ertugrul Filiz

E-Mail Website
Guest Editor
Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750 Duzce, Turkey
Interests: plant biotechnology; computational molecular biology; bioinformatics applications in plants; abiotic stress tolerance in plant; membrane transport proteins in plants

Special Issue Information

Dear Colleagues,

The discovery of high-throughput sequencing (HTS) and its employment in genomics, transcriptomics and other omics disciplines paved the way for the production of a staggering amount of big biological data. The inference of meaningful results from ever-increasing biological data regarding structures and functions of genes, their evolutions over time, protein–protein or protein–ligand interactions and to shed light on metabolic processes and pathways all depend on the effective and accurate processing of big biological data. In this context, bioinformatics plays a major role in deciphering behaviors, interactions and networks of biological molecules and structures. Today, the employment of neural network methods under artificial intelligence and machine learning gives further impetus to understand living systems through more efficient and effective data mining and data processing of the accumulated biological big data.

With this Special Issue, I wish to invite the submission of high-quality original research manuscripts or review articles on any topic related to: “Application of Bioinformatics in Plants”.

In order to contribute to the understanding of the complex molecular worlds of plants, I request you to submit your research and join in our Special Issue.

You will find all the necessary information and instructions and a team up to the task at the Genes editorial office. 

Prof. Dr. Ertugrul Filiz
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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • genome-wide analyses
  • comparative transcriptomics
  • comparative transcriptome meta-analysis
  • phylogenomics and evolutionary analyses
  • gene co-expression network analysis
  • machine learning in plant science
  • comparative genomics
  • protein sequence analyses and 3D modeling
  • molecular docking analysis
  • virtual screening for drug discovery

Published Papers (5 papers)

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Research

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15 pages, 5508 KiB  
Article
Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development
by Muhammad Khuram Razzaq, Reena Rani, Guangnan Xing, Yufei Xu, Ghulam Raza, Muqadas Aleem, Shahid Iqbal, Muhammad Arif, Zahid Mukhtar, Henry T. Nguyen, Rajeev K. Varshney, Kadambot H. M. Siddique and Junyi Gai
Genes 2023, 14(6), 1254; https://doi.org/10.3390/genes14061254 - 12 Jun 2023
Cited by 1 | Viewed by 2041
Abstract
The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We [...] Read more.
The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I–XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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12 pages, 3183 KiB  
Article
Genome-Wide Identification of NAC Gene Family and Expression Analysis under Abiotic Stresses in Avena sativa
by Lei Ling, Mingjing Li, Naiyu Chen, Xinying Xie, Zihui Han, Guoling Ren, Yajie Yin and Huixin Jiang
Genes 2023, 14(6), 1186; https://doi.org/10.3390/genes14061186 - 29 May 2023
Cited by 2 | Viewed by 1450
Abstract
In this study, a total of 177 NAC members were identified in Avena sativa, located on 21 chromosomes. Phylogenetic analysis showed that AsNAC proteins could be divided into seven subfamilies (I–VII), and that proteins in the same subfamily have similar protein motifs. Gene [...] Read more.
In this study, a total of 177 NAC members were identified in Avena sativa, located on 21 chromosomes. Phylogenetic analysis showed that AsNAC proteins could be divided into seven subfamilies (I–VII), and that proteins in the same subfamily have similar protein motifs. Gene structure analysis found that NAC introns ranged from 1 to 17. Cis-element analysis of the promoter indicated that the gene family may have stress-related elements and growth regulation elements. Through qRT-PCR experiments, we speculated that AsNACs genes can respond to abiotic stresses such as cold, freezing, salt, and saline alkali. This study provides a theoretical basis for further exploring the function of the NAC gene family in A. sativa. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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17 pages, 5720 KiB  
Article
Proteome Dynamics Analysis Reveals the Potential Mechanisms of Salinity and Drought Response during Seed Germination and Seedling Growth in Tamarix hispida
by Xin’an Pang, Shuo Liu, Jiangtao Suo, Tiange Yang, Samira Hasan, Ali Hassan, Jindong Xu, Sushuangqing Lu, Sisi Mi, Hong Liu and Jialing Yao
Genes 2023, 14(3), 656; https://doi.org/10.3390/genes14030656 - 05 Mar 2023
Cited by 1 | Viewed by 1395
Abstract
Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the [...] Read more.
Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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15 pages, 2444 KiB  
Article
Genome-Wide Identification, Characterization and Expression Profiling of Potato (Solanum tuberosum) Frataxin (FH) Gene
by Firat Kurt, Ertugrul Filiz, Kubra Yildiz and M. Aydın Akbudak
Genes 2023, 14(2), 468; https://doi.org/10.3390/genes14020468 - 11 Feb 2023
Viewed by 1427
Abstract
Frataxin (FH) plays a crucial role in the biogenesis of mitochondria and the regulation of iron in the cells of various organisms. However, there has been very little research on FH in plants. In this study, the potato FH gene (StFH) [...] Read more.
Frataxin (FH) plays a crucial role in the biogenesis of mitochondria and the regulation of iron in the cells of various organisms. However, there has been very little research on FH in plants. In this study, the potato FH gene (StFH) was identified and characterized using a genome-wide approach, and its sequence was compared to those of FH genes from Arabidopsis, rice, and maize. The FH genes were found to have a lineage-specific distribution and were more conserved in monocots than in dicots. While multiple copies of FH genes have been reported in some species, including plants, only one isoform of FH was found in potato. The expression of StFH in leaves and roots was analyzed under two different abiotic stress conditions, and the results showed that StFH was upregulated more in leaves and that its expression levels increased with the severity of the stress. This is the first study to examine the expression of an FH gene under abiotic stress conditions. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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15 pages, 6420 KiB  
Technical Note
A Multigraph-Based Representation of Hi-C Data
by Diána Makai, András Cseh, Adél Sepsi and Szabolcs Makai
Genes 2022, 13(12), 2189; https://doi.org/10.3390/genes13122189 - 23 Nov 2022
Viewed by 2100
Abstract
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to [...] Read more.
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to environmental stimuli, the linear sequence information needs to be interpreted in three-dimensional space, which is still a challenging task. Here, we propose a novel, heuristic approach to represent Hi-C datasets by a whole-genomic pseudo-structure in 3D space. The baseline of our approach is the construction of a multigraph from genomic-sequence data and Hi-C interaction data, then applying a modified force-directed layout algorithm. The resulting layout is a pseudo-structure. While pseudo-structures are not based on direct observation and their details are inherent to settings, surprisingly, they demonstrate interesting, overall similarities of known genome structures of both barley and rice, namely, the Rabl and Rosette-like conformation. It has an exciting potential to be extended by additional omics data (RNA-seq, Chip-seq, etc.), allowing to visualize the dynamics of the pseudo-structures across various tissues or developmental stages. Furthermore, this novel method would make it possible to revisit most Hi-C data accumulated in the public domain in the last decade. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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