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Molecular Biology and Bioinformatics of Forest Trees—2nd Edition
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Molecular Biology and Bioinformatics of Forest Trees—2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 3981

Special Issue Editors

Dr. Shijiang Cao

E-Mail Website
Guest Editor
College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: forest molecular biology; tree physiology; plant developmental biology; plant-microbe interactions
Special Issues, Collections and Topics in MDPI journals
Dr. Linkun Wu

E-Mail Website
Guest Editor
College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: plant microbiome; replant disease; plant-soil feedback; rhizosphere ecology; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, entitled "Molecular Biology and Bioinformatics of Forest Trees—2nd Edition", aims to delve into the underlying genetic mechanisms and molecular processes that regulate the growth, development, and adaptability of forest trees. Through an in-depth exploration of molecular biology techniques such as DNA sequencing, gene expression profiling, and proteomics, researchers can gain insights into the intricate molecular networks and pathways within trees.

Moreover, this Special Issue underscores the pivotal role of bioinformatics in forestry research. Bioinformatics facilitates the management and analysis of vast genomic datasets, empowering researchers to derive valuable insights through computational methods. Understanding the complex relationships between plants and microbes is also crucial for unraveling the dynamics of forest ecosystems. By leveraging bioinformatics, researchers can analyze the intricate interaction networks between forest trees and microbes, deciphering the key genes, metabolic pathways, and signaling cascades involved.

In summary, this Special Issue places particular emphasis on molecular biology and bioinformatics, while also welcoming research on plant–microbe interactions. It aims to provide novel insights and methodologies that deepen our understanding of forest tree genetics, enhance breeding strategies, and support sustainable forest management practices. We look forward to receiving contributions that collectively advance this field.

Dr. Shijiang Cao
Dr. Linkun Wu
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 250 words) can be sent to the Editorial Office for assessment.

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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • forest molecular biology
  • bioinformatics
  • tree genetics
  • gene expression regulation
  • plant–microbe interactions

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Related Special Issue

Published Papers (3 papers)

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15 pages, 10961 KB  
Article
Integrative Transcriptomics Reveals Regulatory Networks Underlying Fatty Acid and Lacquer Wax Formation in Fruit of Toxicodendron vernicifluum
by Shasha Li, Yufen Xie, Xiao Zhang, Xuan Wang, Xiaomin Ge, Junhui Zhou, Chen Chen and Guoqing Bai
Plants 2026, 15(1), 121; https://doi.org/10.3390/plants15010121 - 1 Jan 2026
Viewed by 480
Abstract
The lacquer tree (Toxicodendron vernicifluum) possesses significant economic value due to its capability to produce raw lacquer, lacquer wax, and lacquer oil. The fruit is the primary source of lacquer wax; the primary components of lacquer wax are fatty acids, yet [...] Read more.
The lacquer tree (Toxicodendron vernicifluum) possesses significant economic value due to its capability to produce raw lacquer, lacquer wax, and lacquer oil. The fruit is the primary source of lacquer wax; the primary components of lacquer wax are fatty acids, yet the synthesis mechanisms of fatty acids and wax esters remain unclear. In this study, we employed RNA-seq to analyze differentially expressed genes (DEGs) across four developmental stages in the fruit of the lacquer tree. The results revealed that, compared to the T1 stage, there were 1736, 10,228, and 12,444 DEGs in the three developmental stages. Through KEGG enrichment analysis, DEGs associated with lacquer wax synthesis were found to be primarily enriched in fatty acid metabolism, degradation, and the biosynthesis of cutin, suberin, and wax esters pathways. Furthermore, analysis of DEGs expression patterns in fatty acid synthesis pathways revealed that ACC, KAS, KAR, FATB, and FAD were significantly differentially expressed. Additionally, LACS, WSD1, CER4, CER1, and MAH1 participated in wax biosynthesis. Moreover, one co-expression network among wax biosynthesis genes, hormone signal transduction genes, and transcription factors was established. These findings provide a theoretical foundation for identifying key genes involved in regulating fatty acid and lacquer wax synthesis in Toxicodendron vernicifluum. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees—2nd Edition)
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17 pages, 3544 KB  
Article
Assembly and Analysis of the Mitochondrial Genome of Hippophae rhamnoides subsp. sinensis, an Important Ecological and Economic Forest Tree Species in China
by Jie Li, Song-Song Lu, Yang Bi, Yu-Mei Jiang, Li-Dan Feng and Jing He
Plants 2025, 14(14), 2170; https://doi.org/10.3390/plants14142170 - 14 Jul 2025
Cited by 1 | Viewed by 1268
Abstract
Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional [...] Read more.
Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees—2nd Edition)
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18 pages, 3658 KB  
Article
Genome-Wide Analysis of CPP Transcription Factor Family in Endangered Plant Phoebe bournei and Its Response to Adversity
by Ronglin Liu, Yizhuo Feng, Qingyan Li, Hua Wu, Shengzhou Guo, Junnan Li, Xiaomin Liu, Yanlin Zhang, Xinghao Tang and Shijiang Cao
Plants 2025, 14(5), 803; https://doi.org/10.3390/plants14050803 - 5 Mar 2025
Cited by 3 | Viewed by 1589
Abstract
The CPP gene family comprises transcription factor genes containing a conserved CRC domain, which is mainly involved in plant development and evolution. Although CPP genes have been widely studied in many plants, little is known about them in woody plants, especially in the [...] Read more.
The CPP gene family comprises transcription factor genes containing a conserved CRC domain, which is mainly involved in plant development and evolution. Although CPP genes have been widely studied in many plants, little is known about them in woody plants, especially in the endangered species Phoebe bournei (Hemsl.). In the genome of Phoebe bournei, we identified 11 PbCPP genes (PbCPP1-PbCPP11) distributed on four chromosomes, with large differences in the number of amino acids. They encode both acidic and alkaline proteins. A phylogenetic analysis showed that these PbCPP genes can be divided into three subfamilies, A, B, and C, which contain seven, two, and two genes, respectively. Through an interspecific collinearity analysis, we identified homologous PbCPP genes. A promoter cis-acting element analysis revealed that PbCPPs contain a variety of elements that respond to plant hormones, stress signals, and light and play a role in growth and development, and most PbCPP genes (except PbCPP3 and PbCPP8) contain MYB binding site elements that regulate drought-induced stress responses, indicating that they play an important role in plant drought resistance. An expression analysis showed that PbCPP3 and PbCPP4 expression was high in the roots and stems and lower in the leaves, whereas the expression of most of the other genes was low in the roots, stems, and leaves. In addition, six representative PbCPP genes were detected using qRT-PCR. The results show significant differences in the expression of PbCPP genes under abiotic stress conditions (drought, cold, and salt), indicating that they play an important role in stress responses. This study preliminarily verified the role of the PbCPP gene family in different abiotic stress responses, which is of great significance for understanding its mechanism in plant growth and development and stress adaptation. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees—2nd Edition)
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