Submit to Special Issue Submit Abstract to Special Issue Review for CIMB Propose a Special Issue

Journal Menu

Journal Browser

Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 November 2024 | Viewed by 7089

Share This Special Issue

Special Issue Editors

Prof. Dr. Quan Zou

E-Mail Website
Guest Editor

Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
Interests: bioinformatics; machine learning; parallel computing
Special Issues, Collections and Topics in MDPI journals

Dr. Ran Su

E-Mail Website
Guest Editor

School of Computer Software, Tianjin University, Tianjin 300350, China
Interests: biomedical image analysis; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the first plant genome, that of Arabidopsis thaliana, was published in December 2000, over 1000 plant genomes representing different plant species and subspecies have been sequenced and published. With the development of sequencing technology, an increasing number of omics datasets have been released, such as pan-genomics, proteomics, transcriptomics and metabolomics. It is important to highlight that the rapid accumulation of omics datasets has greatly promoted the development of plant science, especially crop genetics and breeding. In recent years, even many bioinformatic tools have been developed for omics analyses, but there are still many challenges remaining, from the construction of complex plant genomes to multi-omics analyses. Hence, more advanced algorithms, more powerful pan-genome analysis tools and more comprehensive databases still need to be developed.

Polyploidy, heterozygosity and large genomes in plants are still the main obstacles to plant genome sequencing and assembly; we believe that future studies about omics analyses in plants can make progress by incorporating more advanced technologies. Therefore, we organized this Special Issue on “Comparative Genomics and Functional Genomics Analyses in Plants, 2nd Edition” to help us better understand the plant genome and gene function and evolution and provide a resource for decoding the molecular mechanisms of complex agronomic traits.

I am pleased to invite you to participate in this Special Issue, “Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition”. Research papers, up-to-date review articles, and commentaries are all welcome.

We also thank to Dr. Yansu Wang for her contribution and support of this Special Issue.

Prof. Dr. Quan Zou
Dr. Ran Su
Guest Editors

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. Current Issues in Molecular Biology 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 2200 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

de novo genome sequencing
pan-genomic analyses
genome re-sequencing
GWAS analyses
RNA-seq
metabolomics
gene family analyses
plant evolutionary analyses
bioinformatics
database

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
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 polices can be found here.

Published Papers (7 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

22 pages, 5257 KiB

Open AccessArticle

Mapping the Influence of Light Intensity on the Transgenerational Genetic Architecture of Arabidopsis thaliana

by Jie Mei, Jincan Che, Yunzhu Shi, Yudian Fang, Rongling Wu and Xuli Zhu

Curr. Issues Mol. Biol. 2024, 46(8), 8148-8169; https://doi.org/10.3390/cimb46080482 - 29 Jul 2024

Viewed by 403

Abstract

Light is a crucial environmental factor that influences the phenotypic development of plants. Despite extensive studies on the physiological, biochemical, and molecular mechanisms of the impact of light on phenotypes, genetic investigations regarding light-induced transgenerational plasticity in Arabidopsis thaliana remain incomplete. In this study, we used thaliana as the material, then gathered phenotypic data regarding leaf number and plant height under high- and low-light conditions from two generations. In addition to the developed genotype data, a functional mapping model was used to locate a series of significant single-nucleotide polymorphisms (SNPs). Under low-light conditions, a noticeable adaptive change in the phenotype of leaf number in the second generation suggests the presence of transgenerational genetic effects in thaliana under environmental stress. Under different lighting treatments, 33 and 13 significant genes associated with transgenerational inheritance were identified, respectively. These genes are largely involved in signal transduction, technical hormone pathways, light responses, and the regulation of organ development. Notably, genes identified under high-light conditions more significantly influence plant development, whereas those identified under low-light conditions focus more on responding to external environmental stimuli. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

16 pages, 12413 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Sweet Cherry Whirly Gene Family

by Lili Wang, Qiandong Hou and Guang Qiao

Curr. Issues Mol. Biol. 2024, 46(8), 8015-8030; https://doi.org/10.3390/cimb46080474 - 26 Jul 2024

Viewed by 612

Abstract

Sweet cherry (Prunus avium) is one of the economically valuable horticultural fruit trees and it is widely cultivated throughout the world. Whirly (WHY) genes are a unique gene family with few members and have important biological functions in plant growth, development, and response to abiotic stress. This study utilized whole-genome identification to conduct a comprehensive analysis of the WHY genes in sweet cherry and examined their transcription levels in different tissues and under abiotic stress to explore their functions. Two WHY genes were identified in the sweet cherry genome and named PavWHY1 and PavWHY2, respectively, based on their homology with those in Arabidopsis thaliana. Both genes have theoretical isoelectric points greater than seven and are hydrophilic proteins, suggesting that they may be localized in plastids. The two genes are evolutionarily classified into two categories, with large differences in gene structure, and highly similar protein tertiary structures, and both have conserved domains of WHY. PavWHY1 and PavWHY2 are collinear with AtWHY1 and AtWHY2, respectively. The promoter sequence contains cis-acting elements related to hormones and abiotic stress, which are differentially expressed during flower bud differentiation, fruit development, and cold accumulation. qRT–PCR showed that PavWHY1 and PavWHY2 were differentially expressed in flower and fruit development and responded to low temperature and exogenous ABA treatment. The recombinant plasmid pGreenII-0800-Luc with the promoters of these two genes can activate luciferase expression in tobacco. Protein interaction predictions indicate that these gene products may interact with other proteins. This study reveals the molecular features, evolutionary relationships, and expression patterns of sweet cherry WHY genes, and investigates the activities of their promoters, which lays the foundation for further exploration of their biological functions and provides new insights into the WHY gene family in Rosaceae. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

19 pages, 8483 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of BrBASS Genes in Brassica rapa Reveals Their Potential Roles in Abiotic Stress Tolerance

by Zhaojing Ji, Ruolan Wang, Meiqi Zhang, Luhan Chen, Yuexin Wang, Jiyun Hui, Shiya Hao, Bingcan Lv, Qiwei Jiang and Yunyun Cao

Curr. Issues Mol. Biol. 2024, 46(7), 6646-6664; https://doi.org/10.3390/cimb46070396 - 28 Jun 2024

Viewed by 936

Abstract

The bile acid sodium symporter (BASS) family plays an important role in transporting substances and coordinating plants’ salt tolerance. However, the function of BASS in Brassica rapa has not yet been elucidated. In this study, eight BrBASS genes distributed on five chromosomes were identified that belonged to four subfamilies. Expression profile analysis showed that BrBASS7 was highly expressed in roots, whereas BrBASS4 was highly expressed in flowers. The promoter element analysis also identified several typical homeopathic elements involved in abiotic stress tolerance and stress-related hormonal responses. Notably, under salt stress, the expression of BrBASS2 was significantly upregulated; under osmotic stress, that of BrBASS4 increased and then decreased; and under cold stress, that of BrBASS7 generally declined. The protein–protein interaction analysis revealed that the BrBASS2 homologous gene AtBASS2 interacted with Nhd1 (N-mediated heading date-1) to alleviate salt stress in plants, while the BrBASS4 homologous gene AtBASS3 interacted with BLOS1 (biogenesis of lysosome-related organelles complex 1 subunit 1) via co-regulation with SNX1 (sorting nexin 1) to mitigate an unfavorable growing environment for roots. Further, Bra-miR396 (Bra-microRNA396) targeting BrBASS4 and BrBASS7 played a role in the plant response to osmotic and cold stress conditions, respectively. This research demonstrates that BrBASS2, BrBASS4, and BrBASS7 harbor great potential for regulating abiotic stresses. The findings will help advance the study of the functions of the BrBASS gene family. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

16 pages, 2856 KiB

Open AccessArticle

Selection of Reference Genes for Expression Normalization by RT-qPCR in Dracocephalum moldavica L.

by Shasha Li, Xiaomin Ge, Guoqing Bai and Chen Chen

Curr. Issues Mol. Biol. 2024, 46(6), 6284-6299; https://doi.org/10.3390/cimb46060375 - 20 Jun 2024

Cited by 1 | Viewed by 500

Abstract

Dracocephalum moldavica is widely used as an ornamental, medicine, and perfume in industry. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) is widely and accurately utilized for gene expression evaluations. Selecting optimal reference genes is essential for normalizing RT-qPCR results. However, the identification of suitable reference genes in D. moldavica has not been documented. A total of 12 reference genes in D. moldavica were identified by PEG6000 (15%) treatment under hypertonia conditions in different tissues (roots, stem, leaves, flower, seeds and sepal) and during three stages of flower development, then used to validate the expression stability. There were four algorithms (delta Ct, geNorm, NormFinder, and BestKeeper) used to analyze the stability. Finally, the RefFinder program was employed to evaluate the candidate reference genes’ stability. The results showed that ACTIN, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and EF1α (elongation factor-1α) were stable reference genes under the PEG6000 treatment. Heat shock protein 70 (HSP70) was the most stable gene across different flower development stages. ADP-ribosylation factor (ARF) was the most stable gene in different tissues and total samples. This study provides reliable gene expression studies for future research in D. moldavica. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

14 pages, 4610 KiB

Open AccessArticle

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

by Shengpeng Chen, Huai Yang, Yongle Zhang, Chen Chen, Tianheng Ren, Feiquan Tan and Peigao Luo

Curr. Issues Mol. Biol. 2024, 46(1), 11-24; https://doi.org/10.3390/cimb46010002 - 19 Dec 2023

Viewed by 1008

Abstract

Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

18 pages, 3213 KiB

Open AccessArticle

Enhanced UV-B Radiation in Potato Stems and Leaves Promotes the Accumulation of Anthocyanins in Tubers

by Lingyan Cui, Maoxing Li, Xing Zhang, Zongming Guo, Kaifeng Li, Yuhan Shi, Qiong Wang and Huachun Guo

Curr. Issues Mol. Biol. 2023, 45(12), 9943-9960; https://doi.org/10.3390/cimb45120621 - 11 Dec 2023

Viewed by 1419

Abstract

Enhanced ultraviolet-B (UV-B) radiation promotes anthocyanin biosynthesis in leaves, flowers and fruits of plants. However, the effects and underlying mechanisms of enhanced UV-B radiation on the accumulation of anthocyanins in the tubers of potatoes (Solanum tuberosum L.) remain unclear. Herein, reciprocal grafting experiments were first conducted using colored and uncolored potatoes, demonstrating that the anthocyanins in potato tubers were synthesized in situ, and not transported from the leaves to the tubers. Furthermore, the enhanced UV-B radiation (2.5 kJ·m⁻²·d⁻¹) on potato stems and leaves significantly increased the contents of total anthocyanin and monomeric pelargonidin and peonidin in the red-fleshed potato ‘21-1’ tubers, compared to the untreated control. A comparative transcriptomic analysis showed that there were 2139 differentially expressed genes (DEGs) under UV-B treatment in comparison to the control, including 1724 up-regulated and 415 down-regulated genes. The anthocyanin-related enzymatic genes in the tubers such as PAL, C4H, 4CL, CHS, CHI, F3H, F3’5’H, ANS, UFGTs, and GSTs were up-regulated under UV-B treatment, except for a down-regulated F3’H. A known anthocyanin-related transcription factor StbHLH1 also showed a significantly higher expression level under UV-B treatment. Moreover, six differentially expressed MYB transcription factors were remarkably correlated to almost all anthocyanin-related enzymatic genes. Additionally, a DEGs enrichment analysis suggested that jasmonic acid might be a potential UV-B signaling molecule involved in the UV-B-induced tuber biosynthesis of anthocyanin. These results indicated that enhanced UV-B radiation in potato stems and leaves induced anthocyanin accumulation in the tubers by regulating the enzymatic genes and transcription factors involved in anthocyanin biosynthesis. This study provides novel insights into the mechanisms of enhanced UV-B radiation that regulate the anthocyanin biosynthesis in potato tubers. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Figure 1

Review

Jump to: Research

12 pages, 808 KiB

Open AccessReview

Advances in Genome Sequencing and Natural Rubber Biosynthesis in Rubber-Producing Plants

by Yingchao Tan, Jie Cao, Chaorong Tang and Kaiye Liu

Curr. Issues Mol. Biol. 2023, 45(12), 9342-9353; https://doi.org/10.3390/cimb45120585 - 21 Nov 2023

Cited by 1 | Viewed by 1679

Abstract

Natural rubber (cis-1,4-polyisoprene, NR) is an important raw material utilized widely in the manufacturing of medical, agricultural, and industrial products. Rubber tree (Hevea brasiliensis) and several alternative rubber-producing plants (Taraxacum kok-saghyz, Lactuca sativa, and Parthenium argentatum) have the capability to produce high-quality NR. With the progress of genome sequencing, similar rubber biosynthesis pathways have been discovered among different rubber-producing plant species. NR is synthesized and stored in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The rubber transferase complex is considered to be the pivotal enzyme involved in catalyzing NR biosynthesis. However, the exact compositions of the RT complex in rubber-producing plants remain elusive and poorly understood. Here, we review the progress of genome sequencing, natural rubber biosynthesis, and the components of the RT complex in rubber-producing plants. We emphasize that identifying the detailed components of the RT complex holds great significance for exploring the mechanism of NR biosynthesis and accelerating molecular breeding in rubber-producing plants. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

► Show Figures

Journal Menu

Journal Browser

Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (7 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI