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Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants: 2nd Edition

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

Deadline for manuscript submissions: 20 September 2025 | Viewed by 2908

Special Issue Editor

Prof. Dr. Xiaoming Song

E-Mail Website
Guest Editor
School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
Interests: plant genome evolution; comparative genomics; gene family; RNA-seq; expression network; non-coding RNA; database construction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants play critical roles in human daily life, which have important economic value, medicinal value and ornamental value. With the development of sequencing technology, genome sequencing of more and more horticultural plants has been completed. Moreover, the quality of the released genomes has been obviously improved due to the widely used of third-generation sequencing and Hi-C technology. These genomes provide rich resources for comparative and functional genomic studies in horticultural plants. Therefore, we organize this special issue 2nd Edition to collect relevant research articles to promote the application of omics data in horticultural crops.

This special issue will mainly collect articles from the following aspects, but not limited to these aspects. (a) Gene family analysis at a large-scale level or verified experimentally; (b) Plant genome and comparative genomic analysis; (c) Population evolution and GWAS analysis; (d) Mining and verifying key genes of important agronomic traits; (e) Gene regulatory network construction; (f) Omic resource database or tool development for horticultural plants.

Prof. Dr. Xiaoming Song
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

  • horticultural plants
  • gene family
  • comparative genomics
  • genome evolution
  • gene function
  • gene expression
  • database construction
  • tool development

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Published Papers (3 papers)

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17 pages, 5829 KiB  
Article
Visualized Nucleic Acid Hybridization Lateral Flow Strip Integrating with Microneedle for the Point-of-Care Authentication of Ophiocordyceps sinensis
by Haibin Liu, Xinyue Wang, Hang Tian, Yi Yuan, Jing Wang, Yani Cheng, Linyao Sun, Hongshuo Chen and Xiaoming Song
Int. J. Mol. Sci. 2024, 25(24), 13599; https://doi.org/10.3390/ijms252413599 - 19 Dec 2024
Viewed by 744
Abstract
Due to the price and demand of Ophiocordyceps sinensis having increased dramatically, adulteration with other fungi is a common problem. Thus, a reliable method of authentic O. sinensis identification is essential. In the present work, a rapid DNA extraction and double-tailed recombinase polymerase [...] Read more.
Due to the price and demand of Ophiocordyceps sinensis having increased dramatically, adulteration with other fungi is a common problem. Thus, a reliable method of authentic O. sinensis identification is essential. In the present work, a rapid DNA extraction and double-tailed recombinase polymerase amplification (RPA) coupled with nucleic acid hybridization lateral flow strip (NAH-LFS) was developed to distinguish authentic O. sinensis ingredients from other fungi substitutes. In the presence of O. sinensis, the RPA amplicons with two ssDNA tails in the opposite ends, which could simultaneously bind with the SH-probes on gold nanoparticles (AuNPs) and capture the probe on the test line, formed visible red bands. RPA combined with NAH-LFS can efficiently detect O. sinensis DNA down to 1.4 ng/μL; meanwhile, the specificity test validated no cross reaction with common adulterants, including Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, yungui Cordyceps, and Ophiocordyceps nutans. The whole RPA-NAH-LFS could be completed within 16 min. The RPA-NAH-LFS results in detecting 20 commercial O. sinensis samples are consistent with PCR-AGE and RT-PCR, confirming the feasibility of the RPA-NAH-LFS method. In conclusion, these results are expected to facilitate the application of RPA-NAH-LFS in the authentication detection of O. sinensis materials, providing a convenient and efficient method for O. sinensis quality control. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants: 2nd Edition)
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13 pages, 4590 KiB  
Article
The Role of MaFAD2 Gene in Bud Dormancy and Cold Resistance in Mulberry Trees (Morus alba L.)
by Mengjie Zhao, Gaoxing Zhou, Peigang Liu, Zhifeng Wang, Lu Yang, Tianyan Li, Valiev Sayfiddin Tojiddinovich, Nasirillayev Bakhtiyar Ubaydullayevich, Ismatullaeva Diloram Adilovna, Khudjamatov Safarali Khasanboy Ugl, Yan Liu, Zhiqiang Lv, Jia Wei and Tianbao Lin
Int. J. Mol. Sci. 2024, 25(24), 13341; https://doi.org/10.3390/ijms252413341 - 12 Dec 2024
Cited by 1 | Viewed by 782
Abstract
Bud dormancy is a critical adaptive trait in woody plants, essential for enduring harsh winter conditions. The relationship between bud break timing and cold resistance is complex and has been a subject of debate. This study utilizes a Genome-Wide Association Study (GWAS) on [...] Read more.
Bud dormancy is a critical adaptive trait in woody plants, essential for enduring harsh winter conditions. The relationship between bud break timing and cold resistance is complex and has been a subject of debate. This study utilizes a Genome-Wide Association Study (GWAS) on 201 natural mulberry populations to identify the MaFAD2 gene, which shows the strongest association with bud break timing. Known for its role in cold resistance, MaFAD2′s link to bud break timing suggests a direct correlation between these traits. Expression analysis of MaFAD2 in mulberry trees indicates peak activity in dormant buds, declining as dormancy ends. Selective sweep analysis on germplasms from contrasting climates reveals positive selection in MaFAD2 in cold-resistant Uzbek germplasms. Overexpression of MaFAD2 in early-budding germplasms significantly delays bud break, confirming its regulatory role. These findings highlight MaFAD2 as a key determinant of cold tolerance variability among mulberry germplasms, with its expression directly correlated with bud break timing. This provides a molecular basis for selecting cold-resistant mulberry germplasms based on bud break timing in breeding programs. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants: 2nd Edition)
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17 pages, 7612 KiB  
Article
Characteristics and Expression Analysis of the MYB-Related Subfamily Gene in Rosa chinensis
by Yongjie Zhu, Yuzheng Deng, Yandong Yao, Kangding Yao, Xuejuan Pan, Xuetong Wu, Zhiya Liu, Jitao Zhang, Wanyi Su and Weibiao Liao
Int. J. Mol. Sci. 2024, 25(23), 12854; https://doi.org/10.3390/ijms252312854 - 29 Nov 2024
Viewed by 913
Abstract
MYB-related transcription factors (TFs) subfamily is a subfamily of MYB TFs, which are mainly involved in plant secondary metabolism, growth and development, and stress response. To explore the function of MYB-related subfamily genes in Rosa chinensis, this study systematically analyzed characters of [...] Read more.
MYB-related transcription factors (TFs) subfamily is a subfamily of MYB TFs, which are mainly involved in plant secondary metabolism, growth and development, and stress response. To explore the function of MYB-related subfamily genes in Rosa chinensis, this study systematically analyzed characters of the MYB-related subfamily members in R. chinensis with bioinformatic analysis using the genomic data of R. chinensis and investigated their expression characteristics using quantitative real-time PCR (qRT-PCR). The results show that 100 MYB-related proteins were identified in R. chinensis. Proteins are mainly found in the nucleus. Chromosome localization revealed that all MYB-related genes are mapped to seven chromosomes and are distributed in clusters. Collinear analysis shows that 13 pairs of MYB-related genes had a collinear relationship, indicating R. chinensis may have evolved its MYB-related subfamily gene through fragment duplication. The analysis of motifs and conserved domains shows that Motif 3 is the most conserved motif. There are numerous ABA and MeJA response elements in MYB-related genes. ABA and MeJA treatments significantly shortened the vase life of R. chinensis, while the flower diameter on day 3 was the largest, suggesting that ABA and MeJA might induce MYB-related gene expression during cut flower senescence. The expression of MYB-related genes is tissue specific, most of which show the highest expression levels in petals. Notably, among six plant growth regulator treatments, ABA treatment significantly increased RcMYB002 expression in R. chinensis, suggesting that RcMYB002 may be a crucial gene for ABA response. This study provides a reference for further research on the function of MYB-related genes in R. chinensis. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants: 2nd Edition)
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