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Molecular Biology and Bioinformatics of Forest Trees

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 15547

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Dr. Shijiang Cao

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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
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Dr. Linkun Wu

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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
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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

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Keywords

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

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Molecular Biology and Bioinformatics of Forest Trees—2nd Edition in Plants (1 article)

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Research

17 pages, 2964 KiB

Open AccessArticle

Endogenous Hormone Regulation During Key Developmental Stages of Pinus koraiensis Siebold & Zucc. Ovules

by Xueqing Liu, Xiaoqian Yu and Ling Yang

Plants 2025, 14(5), 637; https://doi.org/10.3390/plants14050637 - 20 Feb 2025

Viewed by 368

Abstract

In this study, the morphological and anatomical characteristics of the growth of the internal ovules and the dynamic changes in the content of endogenous hormones during the development of Korean pine (Pinus koraiensis Siebold & Zucc.) cones were investigated in detail and their interrelationships determined. In addition, morphological examinations, paraffin section, analysis and enzyme immunoassays were performed to observe the growth and development as well as the fertilization stages of the ovules of P. koraiensis from July of the pollination year to June of the following year. From July of the pollination year to May of the next year, the increase in the content of indoleacetic acid (IAA) and gibberellin and a decrease in the content of abscisic acid (ABA) in the pollination year correlated with the division of the gametophyte free nuclei. It was observed that the levels of IAA, ABA, zeatin riboside (ZR) and isopentenyl adenosine (IPA) initially decreased and then increased during overwintering, which was interpreted as a symptom of adaptation of P. koraiensis ovules to low temperatures. At the end of overwintering, the increase in IPA, ZR and ABA levels was associated with the development of the female gametophyte. The week before fertilization was identified as the stage of oocyte division, in which growth-promoting hormones dominate. During the week of fertilization, the increase in the level of growth-inhibiting hormones correlated with fertilization. After fertilization, the increase in the level of growth-promoting hormones also correlated with early embryonic development. The levels of endogenous hormones were observed to change dynamically with the development of P. koraiensis oocytes, indicating their important role. The results of this study provide the morphological and anatomical basis for related studies on the development of the ovarian strobilus in gymnosperms. Full article

(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)

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17 pages, 2486 KiB

Open AccessArticle

Effects of Different Stand Densities on the Composition and Diversity of Soil Microbiota in a Cunninghamia lanceolata Plantation

by Zuyuan Xu, Fei Fan, Qinmin Lin, Shengzhou Guo, Shumao Li, Yunpeng Zhang, Zhiyi Feng, Xingxing Wang, Christopher Rensing, Guangqiu Cao, Linkun Wu and Shijiang Cao

Plants 2025, 14(1), 98; https://doi.org/10.3390/plants14010098 - 1 Jan 2025

Viewed by 788

Abstract

As sustainable forest management gains increasing attention, comprehending the impact of stand density on soil properties and microbial communities is crucial for optimizing forest ecosystem functions. This study employed high-throughput sequencing in conjunction with soil physicochemical analysis to assess the effects of stand density on soil physicochemical properties and microbial community characteristics in Chinese fir plantations, aiming to elucidate the influence of density regulation on ecosystem services. Our results suggested that changes in soil physicochemical properties and microenvironmental conditions were key drivers of soil microbial diversity. Total carbon (TC), soluble nitrogen (SN), and light fraction organic matter decreased with increasing stand density, while total potassium (TK) and available phosphorus (AP) concentrations increased. The plot with a density of 900 trees ha⁻¹ exhibited the highest bacterial diversity, in contrast to the plot with 1500 trees ha⁻¹, which showed the lowest. The dominant microbial taxa were similar across different stand retention densities, with Acidobacteria, Proteobacteria, and Chloroflexi being the predominant bacterial phyla and Ascomycota and Basidiomycota being the main fungal groups. Significant positive correlations were observed between soil microbial community structures and environmental factors, particularly with respect to soil phosphorus and nitrogen content. The present study demonstrated that reduced stand densities modulated soil nutrient content and enhanced bacterial diversity, thereby contributing to a more complex and stable soil ecosystem structure. These insights provide a scientific foundation for optimizing the management of Chinese fir plantations, thereby supporting the sustainable development of forest ecosystems. Full article

(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)

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11 pages, 5992 KiB

Open AccessArticle

Identification of U6 Promoter and Establishment of Gene-Editing System in Larix kaempferi (Lamb.) Carr

by Jun-Xia Xing, Ao-Jie Luo, Xin-Hao Wang, Qi Ding, Ling Yang and Wan-Feng Li

Plants 2025, 14(1), 45; https://doi.org/10.3390/plants14010045 - 26 Dec 2024

Cited by 1 | Viewed by 1195

Abstract

This study aimed to establish a CRISPR/Cas9 gene-editing system for Larix kaempferi (Lamb.) Carr. (Japanese larch). We screened L. kaempferi U6 promoters and used them to drive sgRNA expression in the CRISPR/Cas9 gene-editing system. The L. kaempferi embryogenic callus was used as the receptor material for genetic transformation, and the frequency and types of gene editing were then analyzed. The results showed various mutations in the transgenic materials, including base substitutions and deletions, and the editing frequency ranged from 5% to 14.29%. In summary, we established a CRISPR/Cas9 gene-editing system for L. kaempferi. Our results demonstrate that the CRISPR/Cas9 system can efficiently edit genes in L. kaempferi, with significantly higher editing frequencies observed when sgRNA expression is driven by endogenous LaU6 promoters compared to the exogenous promoter ProAtU6-26. This work provides technical support for the study of L. kaempferi gene functions and genetic improvement. Full article

(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)

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21 pages, 8277 KiB

Open AccessArticle

Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei

by Wenzhuo Lv, Hao Yang, Qiumian Zheng, Wenhai Liao, Li Chen, Yiran Lian, Qinmin Lin, Shuhao Huo, Obaid Ur Rehman, Wei Liu, Kehui Zheng, Yanzi Zhang and Shijiang Cao

Plants 2024, 13(21), 3095; https://doi.org/10.3390/plants13213095 - 3 Nov 2024

Cited by 1 | Viewed by 1249

Abstract

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes—PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15—under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family’s functional characteristics and stress resistance regulation in P. bournei. Full article

(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)

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14 pages, 6075 KiB

Open AccessArticle

Identification of Target Gene and Interacting Protein of Two LaSCL6 Alternative Splicing Variants Provides Novel Insights into Larch Somatic Embryogenesis

by Qiao-Lu Zang, Zha-Long Ye, Li-Wang Qi and Wan-Feng Li

Plants 2024, 13(21), 3072; https://doi.org/10.3390/plants13213072 - 31 Oct 2024

Viewed by 916

Abstract

Somatic embryogenesis is valuable for clonal propagation and genetic improvement, and it also serves as an ideal system for studying plant development mechanisms. In Larix kaempferi, microRNA171 and its target gene L. kaempferi SCARECROW-LIKE6 (LaSCL6), which has two alternative splicing variants, can regulate somatic embryogenesis; however, the underlying molecular mechanism is still unknown. In this study, we overexpressed these two LaSCL6 variants in Oryza sativa and Arabidopsis thaliana and then used the RNA-Seq method to screen genes from O. sativa and A. thaliana, whose expression patterns are related to those of LaSCL6 variants. The screened genes were then used to search L. kaempferi proteins to identify the candidate target genes of LaSCL6. After yeast one-hybrid and dual- luciferase transcriptional activity assays, cytochrome P450, family 89, subfamily A, polypeptide 5 (CYP89A5), and wall-associated receptor kinase-like 20 (WAKL20) were confirmed to be the target genes of LaSCL6-var1; in addition, WAKL20 and UDP-glycosyltransferase 85A3 (UGT85A3) were confirmed to be the target genes of LaSCL6-var2. Moreover, APETALA2-like protein 2, a transcription factor from the AP2/ERF family, was shown to interact with LaSCL6-var1 and LaSCL6-var2. Taken together, our results suggest a regulatory network of miR171-LaSCL6. The findings presented here not only provide novel insights into the regulation of the miR171-LaSCL6 module but also explain the mechanism underlying larch somatic embryogenesis and other biological processes. Full article

(This article belongs to the Special Issue Molecular Biology and Bioinformatics of Forest Trees)

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18 pages, 7825 KiB

Open AccessArticle

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

Cited by 3 | Viewed by 1318

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 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

Open AccessArticle

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 3965

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 1305

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 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

Open AccessArticle

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 3 | Viewed by 1701

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, 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

Open AccessCommunication

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 2 | Viewed by 1551

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 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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