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Molecular Biology and Bioinformatics of Forest Trees
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Molecular Biology and Bioinformatics of Forest Trees

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4521

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
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, titled "Molecular Biology and Bioinformatics of Forest Trees", 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 a strong emphasis on molecular biology and bioinformatics, while also welcoming research on plant–microbe interactions. It aims to provide novel insights and methodologies to deepen our understanding of forest tree genetics, enhance breeding strategies, and support sustainable forest management practices. We eagerly anticipate receiving the contributions of active scholars and researchers to 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 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. 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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Published Papers (5 papers)

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Research

18 pages, 7825 KiB  
Article
Glutamine Synthetase and Glutamate Synthase Family Perform Diverse Physiological Functions in Exogenous Hormones and Abiotic Stress Responses in Pyrus betulifolia Bunge (P.be)
by Weilong Zhang, Shuai Yuan, Na Liu, Haixia Zhang and Yuxing Zhang
Plants 2024, 13(19), 2759; https://doi.org/10.3390/plants13192759 - 1 Oct 2024
Viewed by 478
Abstract
The unscientific application of nitrogen (N) fertilizer not only increases the economic input of pear growers but also leads to environmental pollution. Improving plant N use efficiency (NUE) is the most effective economical method to solve the above problems. The absorption and utilization [...] Read more.
The unscientific application of nitrogen (N) fertilizer not only increases the economic input of pear growers but also leads to environmental pollution. Improving plant N use efficiency (NUE) is the most effective economical method to solve the above problems. The absorption and utilization of N by plants is a complicated process. Glutamine synthetase (GS) and glutamate synthase (GOGAT) are crucial for synthesizing glutamate from ammonium in plants. However, their gene family in pears has not been documented. This study identified 29 genes belonging to the GS and GOGAT family in the genomes of Pyrus betulaefolia (P.be, 10 genes), Pyrus pyrifolia (P.py, 9 genes), and Pyrus bretschneideri (P.br, 10 genes). These genes were classified into two GS subgroups (GS1 and GS2) and two GOGAT subgroups (Fd–GOGAT and NADH–GOGAT). The similar exon–intron structures and conserved motifs within each cluster suggest the evolutionary conservation of these genes. Meanwhile, segmental duplication has driven the expansion and evolution of the GS and GOGAT gene families in pear. The tissue–specific expression dynamics of PbeGS and PbeGOGAT genes suggest significant roles in pear growth and development. Cis–acting elements of the GS and GOGAT gene promoters are crucial for plant development, hormonal responses, and stress reactions. Furthermore, qRT–PCR analysis indicated that PbeGSs and PbeGOGATs showed differential expression under exogenous hormones (GA3, IAA, SA, ABA) and abiotic stress (NO3− and salt stress). In which, the expression of PbeGS2.2 was up–regulated under hormone treatment and down–regulated under salt stress. Furthermore, physiological experiments demonstrated that GA3 and IAA promoted GS, Fd–GOGAT, and NADH–GOGAT enzyme activities, as well as the N content. Correlation analysis revealed a significant positive relationship between PbeGS1.1, PbeGS2.2, PbeNADH–GOGATs, and the N content. Therefore, PbeGS1.1, PbeGS2.2, and PbeNADH–GOGATs could be key candidate genes for improving NUE under plant hormone and abiotic stress response. To the best of our knowledge, our study provides valuable biological information about the GS and GOGAT family in the pear for the first time and establishes a foundation for molecular breeding aimed at developing high NUE pear rootstocks. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)
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17 pages, 5171 KiB  
Article
Transcription Factor and Protein Regulatory Network of PmACRE1 in Pinus massoniana Response to Pine Wilt Nematode Infection
by Wanfeng Xie, Xiaolin Lai, Yuxiao Wu, Zheyu Li, Jingwen Zhu, Yu Huang and Feiping Zhang
Plants 2024, 13(19), 2672; https://doi.org/10.3390/plants13192672 - 24 Sep 2024
Viewed by 662
Abstract
Pine wilt disease, caused by Bursaphelenchus xylophilus, is a highly destructive and contagious forest affliction. Often termed the “cancer” of pine trees, it severely impacts the growth of Masson pine (Pinus massoniana). Previous studies have demonstrated that ectopic expression of [...] Read more.
Pine wilt disease, caused by Bursaphelenchus xylophilus, is a highly destructive and contagious forest affliction. Often termed the “cancer” of pine trees, it severely impacts the growth of Masson pine (Pinus massoniana). Previous studies have demonstrated that ectopic expression of the PmACRE1 gene from P. massoniana in Arabidopsis thaliana notably enhances resistance to pine wilt nematode infection. To further elucidate the transcriptional regulation and protein interactions of the PmACRE1 in P. massoniana in response to pine wilt nematode infection, we cloned a 1984 bp promoter fragment of the PmACRE1 gene, a transient expression vector was constructed by fusing this promoter with the reporter GFP gene, which successfully activated the GFP expression. DNA pull-down assays identified PmMYB8 as a trans-acting factor regulating PmACRE1 gene expression. Subsequently, we found that the PmACRE1 protein interacts with several proteins, including the ATP synthase CF1 α subunit, ATP synthase CF1 β subunit, extracellular calcium-sensing receptor (PmCAS), caffeoyl-CoA 3-O-methyltransferase (PmCCoAOMT), glutathione peroxidase, NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase 1, cinnamyl alcohol dehydrogenase, auxin response factor 16, and dehydrin 1 protein. Bimolecular fluorescence complementation (BiFC) assays confirmed the interactions between PmACRE1 and PmCCoAOMT, as well as PmCAS proteins in vitro. These findings provide preliminary insights into the regulatory role of PmACRE1 in P. massoniana’s defense against pine wilt nematode infection. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)
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15 pages, 3936 KiB  
Article
Altitudinal Effects on Soil Microbial Diversity and Composition in Moso Bamboo Forests of Wuyi Mountain
by Yiming Sun, Xunlong Chen, Jianwei Cai, Yangzhuo Li, Yuhan Zhou, Houxi Zhang and Kehui Zheng
Plants 2024, 13(17), 2471; https://doi.org/10.3390/plants13172471 - 4 Sep 2024
Viewed by 590
Abstract
Moso bamboo (Phyllostachys edulis) forest is a key ecosystem and its soil microbial community plays a crucial role in maintaining the ecosystem’s functions, but it is very vulnerable to climate change. An altitude gradient can positively simulate environmental conditions caused by [...] Read more.
Moso bamboo (Phyllostachys edulis) forest is a key ecosystem and its soil microbial community plays a crucial role in maintaining the ecosystem’s functions, but it is very vulnerable to climate change. An altitude gradient can positively simulate environmental conditions caused by climate change, and hence, it provides an efficient means of investigating the response of soil microorganisms to such climatic changes. However, while previous research has largely concentrated on plant–soil–microorganism interactions across broad altitudinal ranges encompassing multiple vegetation types, studies examining these interactions within a single ecosystem across small altitudinal gradients remain scarce. This study took Moso bamboo forests at different altitudes in Wuyi Mountain, China, as the research object and used high-throughput sequencing technology to analyze the soil microbial community structure, aiming to elucidate the changes in soil microbial communities along the altitude gradient under the same vegetation type and its main environmental driving factors. This study found that the structure of bacterial community was notably different in Moso bamboo forests’ soil at varying altitudes, unlike the fungal community structure, which showed relatively less variance. Bacteria from Alphaproteobacteria phylum were the most dominant (14.71–22.91%), while Agaricomycetes was the most dominating fungus across all altitudinal gradients (18.29–30.80%). Fungal diversity was higher at 530 m and 850 m, while bacterial diversity was mainly concentrated at 850 m and 1100 m. Redundancy analysis showed that soil texture (sand and clay content) and available potassium content were the main environmental factors affecting fungal community structure, while clay content, pH, and available potassium content were the main drivers of bacterial community structure. This study demonstrates that the altitude gradient significantly affects the soil microbial community structure of Moso bamboo forest, and there are differences in the responses of different microbial groups to the altitude gradient. Soil properties are important environmental factors that shape microbial communities. The results of this study contribute to a deeper understanding of the impact of altitude gradient on the soil microbial community structure of Moso bamboo forests, thus providing support for sustainable management of Moso bamboo forests under climate change scenarios. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)
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15 pages, 3642 KiB  
Article
Comparative Genome-Wide Identification of the Fatty Acid Desaturase Gene Family in Tea and Oil Tea
by Ziqi Ye, Dan Mao, Yujian Wang, Hongda Deng, Xing Liu, Tongyue Zhang, Zhiqiang Han and Xingtan Zhang
Plants 2024, 13(11), 1444; https://doi.org/10.3390/plants13111444 - 23 May 2024
Cited by 1 | Viewed by 1028
Abstract
Camellia oil is valuable as an edible oil and serves as a base material for a range of high-value products. Camellia plants of significant economic importance, such as Camellia sinensis and Camellia oleifera, have been classified into sect. Thea and sect. Oleifera [...] Read more.
Camellia oil is valuable as an edible oil and serves as a base material for a range of high-value products. Camellia plants of significant economic importance, such as Camellia sinensis and Camellia oleifera, have been classified into sect. Thea and sect. Oleifera, respectively. Fatty acid desaturases play a crucial role in catalyzing the formation of double bonds at specific positions of fatty acid chains, leading to the production of unsaturated fatty acids and contributing to lipid synthesis. Comparative genomics results have revealed that expanded gene families in oil tea are enriched in functions related to lipid, fatty acid, and seed processes. To explore the function of the FAD gene family, a total of 82 FAD genes were identified in tea and oil tea. Transcriptome data showed the differential expression of the FAD gene family in mature seeds of tea tree and oil tea tree. Furthermore, the structural analysis and clustering of FAD proteins provided insights for the further exploration of the function of the FAD gene family and its role in lipid synthesis. Overall, these findings shed light on the role of the FAD gene family in Camellia plants and their involvement in lipid metabolism, as well as provide a reference for understanding their function in oil synthesis. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)
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11 pages, 2913 KiB  
Communication
Overexpression of Larch SCL6 Inhibits Transitions from Vegetative Meristem to Inflorescence and Flower Meristem in Arabidopsis thaliana (L.) Heynh.
by Jun-Xia Xing, Qiao-Lu Zang, Zha-Long Ye, Li-Wang Qi, Ling Yang and Wan-Feng Li
Plants 2024, 13(9), 1232; https://doi.org/10.3390/plants13091232 - 29 Apr 2024
Cited by 1 | Viewed by 1096
Abstract
SCARECROW-LIKE6 (SCL6) plays a role in the formation and maintenance of the meristem. In Larix kaempferi (Lamb.) Carr., an important afforestation tree species in China, SCL6 (LaSCL6) has two alternative splicing variants—LaSCL6-var1 and LaSCL6-var2—which are regulated by [...] Read more.
SCARECROW-LIKE6 (SCL6) plays a role in the formation and maintenance of the meristem. In Larix kaempferi (Lamb.) Carr., an important afforestation tree species in China, SCL6 (LaSCL6) has two alternative splicing variants—LaSCL6-var1 and LaSCL6-var2—which are regulated by microRNA171. However, their roles are still unclear. In this study, LaSCL6-var1 and LaSCL6-var2 were transformed into the Arabidopsis thaliana (L.) Heynh. genome, and the phenotypic characteristics of transgenic A. thaliana, including the germination percentage, root length, bolting time, flower and silique formation times, inflorescence axis length, and branch and silique numbers, were analyzed to reveal their functions. It was found that LaSCL6-var1 and LaSCL6-var2 overexpression shortened the root length by 41% and 31%, respectively, and increased the inflorescence axis length. Compared with the wild type, the bolting time in transgenic plants was delayed by approximately 2–3 days, the first flower and silique formation times were delayed by approximately 3–4 days, and the last flower and silique formation times were delayed by about 5 days. Overall, the life cycle in transgenic plants was prolonged by approximately 5 days. These results show that LaSCL6 overexpression inhibited the transitions from the vegetative meristem to inflorescence meristem and from the flower meristem to meristem arrest in A. thaliana, revealing the roles of LaSCL6-var1 and LaSCL6-var2 in the fate transition and maintenance of the meristem. Full article
(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)
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