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Bioinformatics of Plant
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Bioinformatics of Plant

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (5 December 2024) | Viewed by 2509

Special Issue Editor

Dr. Ritesh Kumar

E-Mail Website
Guest Editor
Department of Geology, Kansas State University, Manhattan, KS, USA
Interests: plant molecular biology; abiotic stress; rice; arabidopsis; plant reproduction

Special Issue Information

Dear Colleagues,

We are pleased to announce a special issue of the journal Genes dedicated to advancements in Plant Bioinformatics. This special issue aims to bring together cutting-edge research and reviews that showcase the latest developments, tools, and applications in the field of bioinformatics as it pertains to plant science.

Scope of the Special Issue:

This special issue will cover a wide range of topics within plant bioinformatics, including but not limited to:

  1. Genome Sequencing and Assembly:
    • Innovations in high-throughput sequencing technologies for plant genomes.
    • Advanced algorithms for the assembly and annotation of complex plant genomes.
  2. Functional Genomics:
    • Techniques for gene annotation and the prediction of gene function.
    • Transcriptomic and proteomic analyses to explore gene expression and protein function.
    • Integrative approaches for linking genotype to phenotype in plants.
  3. Comparative and Evolutionary Genomics:
    • Comparative genomic studies that reveal evolutionary relationships and genetic diversity among plant species.
    • Phylogenetic analyses to uncover the evolutionary history of plant genomes.
  4. Structural Genomics:
    • Studies on the 3D organization of plant genomes and its impact on gene regulation.
    • Insights into chromatin dynamics and nuclear architecture in plants.
  5. Systems Biology:
    • Network analysis and modeling of complex biological interactions in plants.
    • Pathway mapping and analysis to understand metabolic and signaling pathways.
  6. Marker-Assisted Selection and Crop Improvement:
    • Development and application of genetic markers in plant breeding programs.
    • Bioinformatics approaches to identify and select desirable traits in crops.
  7. Bioinformatics Tools and Databases:
    • Novel software tools and databases designed for plant genomic data analysis.
    • Advances in computational methods for sequence alignment, variant calling, and functional annotation.
  8. Applications of Plant Bioinformatics:
    • Case studies demonstrating the application of bioinformatics in crop improvement, plant pathology, environmental adaptation, and biodiversity conservation.

Submission Guidelines:

We invite researchers to submit original research articles, reviews, and methodological papers that align with the themes of this special issue. Manuscripts should be prepared according to the journal’s standard guidelines and submitted through the online submission system.

Dr. Ritesh Kumar
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

  • plant genomics
  • genome sequencing
  • genome assembly
  • gene annotation
  • transcriptomics
  • proteomics
  • comparative genomics
  • phylogenetics
  • evolutionary genomics
  • structural genomics
  • 3D genome architecture
  • chromatin dynamics
  • systems biology
  • biological networks

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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23 pages, 3242 KiB  
Article
Profiling of Known and Novel microRNAs in an Oleaginous Crop Native to the Amazon Basin, Sacha Inchi (Plukenetia volubilis), Through smallRNA-Seq
by Richard Estrada, Lila Rodriguez, Yolanda Romero, Linda Arteaga, Domingo Ruelas-Calloapaza, Filiberto Oha-Humpiri, Nils Flores, Pedro Coila and Carlos I. Arbizu
Genes 2025, 16(4), 417; https://doi.org/10.3390/genes16040417 - 31 Mar 2025
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Abstract
Background: MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in Plukenetia volubilis (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: [...] Read more.
Background: MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in Plukenetia volubilis (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: root, stem, and leaf. Methods: Small RNA libraries were sequenced on the Illumina Novaseq 6000 platform, yielding high-quality reads that facilitated the discovery of known and novel miRNAs using miRDeep-P. Results: A total of 277 miRNAs were identified, comprising 71 conserved and 206 novel miRNAs, across root, stem, and leaf tissues. In addition, differential expression analysis using DESeq2 identified distinct miRNAs exhibiting tissue-specific regulation. Notably, novel miRNAs like novel_1, novel_88, and novel_189 showed significant roles in processes such as auxin signaling, lignin biosynthesis, and stress response. Functional enrichment analysis of miRNA target genes revealed pathways related to hormonal regulation, structural reinforcement, and environmental adaptation, highlighting tissue-specific functions. The Principal Component Analysis and PERMANOVA confirmed clear segregation of miRNA expression profiles among tissues, underlining organ-specific regulation. Differential expression patterns emphasized unique regulatory roles in each organ: roots prioritized stress response and nutrient uptake, leaves focused on photosynthesis and UV protection, and stems contributed to structural integrity and nutrient transport, suggesting evolutionary adaptations in P. volubilis. Conclusions: This study identified novel miRNA-mediated networks that regulate developmental and adaptive processes in P. volubilis, underscoring its molecular adaptations for resilience and productivity. By characterizing both conserved and novel miRNAs, the findings lay a foundation for genetic improvement and molecular breeding strategies aimed at enhancing agronomic traits, stress tolerance, and the production of bioactive compounds. Full article
(This article belongs to the Special Issue Bioinformatics of Plant)
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16 pages, 7359 KiB  
Article
Comprehensive Evaluation of Cryptic Juglans Genotypes: Insight from Molecular Markers and Phylogenetic Analysis
by Sajjad Sajjad, Muhammad Islam, Khushi Muhammad, Sajid-ul Ghafoor, Irfan Ullah, Asif Khan, Muhammad Siraj, Abdulwahed Fahad Alrefaei, Jawad Ali Shah and Sajid Ali
Genes 2024, 15(11), 1417; https://doi.org/10.3390/genes15111417 - 31 Oct 2024
Viewed by 1923
Abstract
Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes [...] Read more.
Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia ‘Vina’) and (MN397934.1-J. regia ‘Serr’), (MN397933.1 J. regia ‘Pedro’), (MN397932.1 J. regia ‘Lara’), (MN397931.1 J. regia ‘Howard’), and (MN397930.1 J. regia ‘Hartley’) with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia ‘Vina’) and (MN397934.1 J. regia ‘Serr’), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population. Full article
(This article belongs to the Special Issue Bioinformatics of Plant)
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