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19 pages, 2717 KiB

Open AccessArticle

Whole-Genome Identification and Expression Profiles of WRKY Genes Related to the Leaf Expansion Period in the Camphor Tree

by Shilin Long, Jingyao Jiang and Hanyang Lin

Forests 2025, 16(2), 266; https://doi.org/10.3390/f16020266 - 2 Feb 2025

Viewed by 875

Abstract

The camphor tree (Cinnamomum camphora) is of great economic and ecological value, and the WRKY transcription factor (TF) family plays a crucial role in regulating plant growth and development as well as the responses toward environmental changes. However, the research on [...] Read more.

The camphor tree (Cinnamomum camphora) is of great economic and ecological value, and the WRKY transcription factor (TF) family plays a crucial role in regulating plant growth and development as well as the responses toward environmental changes. However, the research on WRKY TFs in C. camphora remains scarce, and their roles in the leaf expansion period are unknown. In this study, we identified WRKY TFs across the C. camphora genome, followed by a phylogenetic analysis. Then, we conducted RNA sequencing and qPCR experiments on leaves collected from three distinct stages during leaf expansion (S1, S2, and S3) to determine which WRKY genes showed significant up-regulation during these stages. Here, a total of 72 CcWRKY TFs were found in the C. camphora genome, and they were phylogenetically clustered with corresponding subfamilies of Arabidopsis thaliana. These CcWRKY proteins were divided into three major groups (I, II, and III), where group II consisted of five subgroups. We found that three genes (CcWRKY24, CcWRKY42, and CcWRKY70) were upregulated from both S1 to S2 and from S1 to S3. The expression level of CcWRKY24 increased gradually from S1 to S3, while CcWRKY42 and CcWRKY70 exhibited higher expression levels in S2 and S3 than in S1. These predicted gene expression profiles were further confirmed by qPCR experiments. In summary, this study analyzed WRKY TFs in C. camphora from a genome-wide perspective and paves the way for future research on the functions of CcWRKYs. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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13 pages, 4580 KiB

Open AccessArticle

Identification of Superoxide Dismutase (SOD) Gene Family in Ginkgo (Ginkgo biloba L.) and Role of GbSOD8 in Response to Salt Stress

by Yuxuan Song, Xinyao Xie, Yuehan Wang, Weijie Gao, Hao Huang, Fuliang Cao and Xiaoming Yang

Forests 2024, 15(12), 2141; https://doi.org/10.3390/f15122141 - 4 Dec 2024

Viewed by 785

Abstract

Superoxide dismutase (SOD), a critical enzyme within the plant antioxidant defense system, serves as the primary shield against reactive oxygen species (ROS) under adverse environmental conditions. However, the characterization of GbSODs in ginkgo remains incomplete. In our study, a total of eight GbSODs [...] Read more.

Superoxide dismutase (SOD), a critical enzyme within the plant antioxidant defense system, serves as the primary shield against reactive oxygen species (ROS) under adverse environmental conditions. However, the characterization of GbSODs in ginkgo remains incomplete. In our study, a total of eight GbSODs were identified, which were unevenly distributed across 10 chromosomes and predominantly localized on the plasma membrane. Our phylogenetic analysis revealed that GbSODs from ginkgo and other species form three distinct groups, each characterized by specific binding domains and supported by relatively high bootstrap values. Our promoter analysis indicated that all GbSODs contained multiple cis-elements related to various abiotic stress responses. Our systemic analysis revealed that only one pair of GbSODs underwent segmental duplications. The transcriptome analysis showed the variable expression of GbSODs across different tissues, which were significantly influenced by drought, ultraviolet (UV), and salt stress, with GbSOD8 showing a particularly notable induction. Transgenic plants that overexpressed GbSOD8 exhibited enhanced antioxidant enzyme activities, elevated proline levels, and reduced malondialdehyde (MDA) content, collectively contributing to their improved salt tolerance compared to wild-type plants. Our findings expand the comprehensive understanding of the GbSOD gene family and provide a solid foundation for further elucidating the molecular mechanisms of GbSODs under salt stress. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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15 pages, 12623 KiB

Open AccessArticle

Genome-Wide Analysis of the MAPKKK Gene Family Under Abiotic Stresses in Moso Bamboo (Phyllostachys edulis)

by Feiyi Huang and Jiaxin Wang

Forests 2024, 15(11), 1883; https://doi.org/10.3390/f15111883 - 25 Oct 2024

Viewed by 801

Abstract

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the upstream components of MAPK cascades and are involved in mediating stress responses and developmental processes. Although MAPKKK genes have been investigated in many plants, the identification and characterization of MAPKKKs in moso bamboo were [...] Read more.

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the upstream components of MAPK cascades and are involved in mediating stress responses and developmental processes. Although MAPKKK genes have been investigated in many plants, the identification and characterization of MAPKKKs in moso bamboo were still limited. Here, 134 MAPKKKs were identified as unevenly distributed on 23 chromosomes (except for chromosome 1) of moso bamboo and divided into three subfamilies by phylogenetic analysis. The gene structure and conserved motif of PeMAPKKKs were investigated. The expansions of PeMAPKKKs were driven by whole-genome duplication (WGD) or segmental duplication events. The duplicated gene pairs were under purifying selection based on the Ka/Ks ratios, suggesting they underwent functional conservation. Most PeMAPKKKs contained cis-elements related to development, hormones, and stress responses. Tissue expression patterns showed that PeMAPKKKs had multiple expression patterns. The qPCR analysis showed distinct expression patterns of PeMAPKKKs under drought, salt, and cold stress conditions. Taken together, this study provides a solid foundation for future functional characterizations of MAPKKKs and identifies candidate stress-responsive genes for further study in moso bamboo. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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18 pages, 6957 KiB

Open AccessArticle

Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis

by Fengyi Liu, Jiarui Zheng, Yuwei Yi, Xiaoyan Yang, Leiyu Jiang, Jiabao Ye, Weiwei Zhang and Feng Xu

Forests 2024, 15(7), 1119; https://doi.org/10.3390/f15071119 - 27 Jun 2024

Viewed by 1411

Abstract

Carotenoids are naturally occurring tetraterpenoids that play a key role in fruit coloration, and yellow peaches are one of the best sources of carotenoid intake. MYB transcription factors are one of the largest families in plants and play an important role in the [...] Read more.

Carotenoids are naturally occurring tetraterpenoids that play a key role in fruit coloration, and yellow peaches are one of the best sources of carotenoid intake. MYB transcription factors are one of the largest families in plants and play an important role in the regulation of plant secondary metabolite biosynthesis. However, peach MYB family genes have not been fully analyzed, and in particular, MYBs that regulate carotenoid biosynthesis have not been fully characterized. In this study, 190 peach MYB genes, containing 68 1R-MYBs, 118 2R-MYBs, 3 3R-MYBs, and 1 4R-MYB, were identified at the genome level using bioinformatics methods. These 190 MYBs were classified into 27 subfamilies based on their phylogenetic relationships with Arabidopsis thaliana MYB family members, and they were unevenly distributed across eight chromosomes. MYB genes of the same subfamily exhibit similar but not identical gene structures and conserved motifs. The promoter regions contain cis-acting elements associated with stress response, hormone response, and plant growth and development. There were 54 collinear pairs of MYB genes in the peach genome, compared with 233 and 221 collinear pairs with Rosa chinensis and Arabidopsis, respectively. Thirteen differentially expressed genes in the carotenoid biosynthesis pathway in yellow peach were identified by transcriptome sequencing and contained MYB binding sites on their promoters. Based on a phylogenetic analysis, we identified 13 PpMYBs that may be involved in carotenoid biosynthesis, and a correlation analysis revealed that they regulate carotenoid accumulation by positively or negatively regulating the expression of carotenoid biosynthetic genes. Further degradome sequencing screened that mdm-miR858 was able to target PpMYB17 and PpMYB126 involved in the regulation of carotenoid biosynthesis. Our findings provide new insights into the potential role of MYB transcription factors in carotenoid biosynthesis and provide a theoretical basis for their molecular mechanisms. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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16 pages, 4354 KiB

Open AccessArticle

Response of Rhododendron simsii and Rhododendron delavayi Superoxide Dismutase Family Genes to High-Temperature Stress

by Xingmin Geng, Li Hua, Jiyi Gong, Yin Yi, Ming Tang and Fanyu Ceng

Forests 2024, 15(6), 931; https://doi.org/10.3390/f15060931 - 27 May 2024

Viewed by 1096

Abstract

Superoxide dismutases (SODs) are the first line of defense in the antioxidant defense system, and they play an essential role in various adversity stress adaptations in Rhododendron. In this study, 9 Rhododendron simsii SODs (RsSODs) and 11 Rhododendron delavayi SODs [...] Read more.

Superoxide dismutases (SODs) are the first line of defense in the antioxidant defense system, and they play an essential role in various adversity stress adaptations in Rhododendron. In this study, 9 Rhododendron simsii SODs (RsSODs) and 11 Rhododendron delavayi SODs (RdSODs) genes were identified in the genomes of R. simsii and R. delavayi. Phylogenetic relationship analysis classified SOD proteins from two Rhododendron species and other related species into three subfamilies. The results of gene structure and conserved motif analysis show that SOD proteins are strongly evolutionarily conserved, and SODs of the same subfamily have similar motif distributions, positions, and lengths. Twenty-two light-responsive elements, eight phytohormone regulatory elements, five adversity stress-related elements, and three growth and development regulatory elements were detected in the RsSOD and RdSOD promoters. Quantitative real-time fluorescence polymerase chain reaction analysis showed that among the 20 candidate genes, except for RdCSD5, the other SODs were expressed in at least one of four tissues, and all of these gene family members had high expression levels in the leaves. We then investigated the response of the RsSOD and RdSOD gene families to high-temperature stress in combination with the following specific stressors: abscisic acid, ethephon, and hydrogen peroxide treatments, followed by high-temperature stress. Different degrees of upregulated expression of the detected SOD gene family members were found for exogenous reagent treatments and different times of high-temperature stress. Thus, we provide a basis for the further functional characterization of SOD genes in R. simsii and R. delavayi in the future. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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18 pages, 5013 KiB

Open AccessArticle

Isolation and Characterization of the Sulfate Transporter Gene Family and Its Expression Pattern in Response to Selenium and Abiotic Stress in Walnuts (Juglans regia L.)

by Simin Zhang, Yansheng Xue, Ningfang Liu, Danzeng Quzhen, De Qiong, Yongling Liao, Weiwei Zhang, Jiabao Ye, Qijian Wang and Feng Xu

Forests 2024, 15(4), 702; https://doi.org/10.3390/f15040702 - 15 Apr 2024

Cited by 3 | Viewed by 1847

Abstract

The sulfate transporter (SULTR) is responsible for the transport and uptake of sulfate, which plays an indispensable role in the growth cycle of plants and adaptation to plant stress. However, there are few reports on the response and regulation of SULTR gene family [...] Read more.

The sulfate transporter (SULTR) is responsible for the transport and uptake of sulfate, which plays an indispensable role in the growth cycle of plants and adaptation to plant stress. However, there are few reports on the response and regulation of SULTR gene family members in walnuts (Juglans regia L.) to sodium selenate, low temperatures, high temperatures, and simulated drought stress. In this study, the whole genome of the SULTR genes family in walnuts was identified and analyzed by the bioinformatics method. The results show that the walnut genome contains seventeen JrSULTR genes, which are unevenly distributed on eight chromosomes and can be divided into four subfamilies. Cis-acting elements that respond to stress and participate in the regulation of plant hormones were found in the promoter sequence of the JrSULTR genes. The analysis of transcriptome data showed that the expression of JrSULTR1.2b was significantly upregulated under sodium selenate treatment, and the results of qRT-PCR analysis were basically consistent with the transcriptome data. The expression of JrSULTR3.1a and JrSULTR3.4b increased with the prolongation of simulated drought stress time. The transcription levels of JrSULTR1.2b and JrSULTR3.1a were significantly increased after low-temperature treatment. After 9 h of high-temperature treatment, the expression levels of JrSULTR3.1a and JrSULTR3.3 were significantly increased. JrSULTR1.2b and JrSULTR3.1a showed significant expression specificity under stress treatment. At the same time, we also performed subcellular localization of these two genes, which was consistent with the predicted results and was in the cell membrane, and their regulatory functions need to be further studied. These studies laid the foundation for us to explore the specific function of the JrSULTR genes in alleviating abiotic stress in walnuts. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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14 pages, 4209 KiB

Open AccessArticle

Identification and Analysis of Expression Patterns of the Caleosin Genes in Hickory (Carya cathayensis Sarg.)

by Yueyinglun Cao, Yang Zhan, Jiale Liu, Tianyu Tang, Juan Li, Rui Zhao, Qixiang Zhang, Shuai Hu, Wenhan Cao and Yanli Gao

Forests 2024, 15(4), 609; https://doi.org/10.3390/f15040609 - 28 Mar 2024

Cited by 2 | Viewed by 1548

Abstract

The deciduous tree hickory (Carya cathayensis) holds economic significance in China due to its high oil content, particularly in unsaturated fatty acids. Oil bodies are crucial for storing triacylglycerol (TAG), with caleosin serving as a predominant oil body protein that aids [...] Read more.

The deciduous tree hickory (Carya cathayensis) holds economic significance in China due to its high oil content, particularly in unsaturated fatty acids. Oil bodies are crucial for storing triacylglycerol (TAG), with caleosin serving as a predominant oil body protein that aids in oil body formation and stability maintenance. Our study utilized bioinformatics techniques to identify caleosin genes within Carya cathayensis, Carya illinoinensis, and Juglans regia. Three caleosin genes were discovered in the genomes of Carya cathayensis, Carya illi-noinensis, and Juglans regia. These genes encode hydrophilic proteins. Additionally, all caleosin proteins feature a single Ca²⁺-binding EF-hand, a conserved “proline knot” motif, and a C-terminal hydrophilic region with four potential phosphorylation sites. The caleosin proteins in Carya cathayensis consist of α-helix, β-corner, extended chain, and random curl structures. Cis-acting elements related to stress response and hormone signaling were identified in Carya cathayensis, Carya illinoinensis, and Juglans regia, with distinct cis-acting elements implicated in seed-specific regulation in Carya cathayensis. Additionally, subcellular localization analysis confirmed that CcaCLO1 and CcaCLO2 were localized within oil bodies. Transcriptome analysis and quantitative real-time polymerase chain reaction (qRT-PCR) data demonstrated a significant up-regulation of CcaCLO1 expression during the developmental stages of the Carya cathayensis embryo. Furthermore, qPCR findings indicated that caleosins from Carya cathayensis were responsive to salt stress, with a significant up-regulation of CcaCLO1 following exposure to salt stress treatment. Consequently, caleosin genes in Carya cathayensis, Carya illinoinensis, and Juglans regia share similar physicochemical characteristics and conserved motifs. Specifically, CcaCLO1 in Carya cathayensis primarily responds to embryo development and salt stress. These findings offer foundational insights for future investigations into the regulatory mechanisms of oil accumulation and response to salt stress in hickory. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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22 pages, 4386 KiB

Open AccessArticle

Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis

by Zhuangyue Lu, Qibo Wang, Zhenxin Yang, Lin Chen, Nianhui Cai and Yulan Xu

Forests 2024, 15(3), 489; https://doi.org/10.3390/f15030489 - 6 Mar 2024

Cited by 5 | Viewed by 1456

Abstract

Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the [...] Read more.

Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the phenotypes of P. yunnanensis seedlings with different plant heights were quite different at their seedling stage, the molecular mechanisms controlling the seedling differentiation remain poorly understood. This study is aimed to investigate the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The P. yunnanensis seedlings were categorized into three grades, i.e., Grades A, B, and C, by mean ± 1/2 standard deviation method (H ± 1/2σ), and the seedling height and ground diameter were measured. We conducted the measurements of endogenous hormone levels in the young shoot apexes of seedlings at different grades during the fast-growth period (March). The DEGs were identified through transcriptome sequencing and analyzed by qRT-PCR validation. Significant differences were observed in the content and ratio of endogenous phytohormones among various grades of P. yunnanensis seedlings (p < 0.05). The ABA content in Grade A was prominently more than that in Grades B and C, and the order of the content of auxins was Grade B > C > A. Furthermore, when compared to Grade A, the ratios of auxins/CTKs, auxins/ABA, CTKs/ABA, and (auxins + CTKs)/ABA exhibited significant increases in Grades B and C. Moreover, GO functional annotation analysis indicated the more pronounced enrichment of DEGs in molecular functions. KEGG metabolic pathway analysis revealed notable differences in enrichment pathways between the pairwise comparisons. The “plant hormone signal transduction” pathway exhibited enrichment in the two groups, followed by “plant–pathogen interaction” pathway in the organism system that was enriched in the three groups. In addition, the results for endogenous phytohormone metabolism pathways indicate a significant up-regulation in the expression of AUX1, while AHP and PP2C exhibited significant down-regulation. To sum up, we aimed at investigating the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The results suggested that individual phytohormones have a limited capacity to regulate gene expression, and seedling differentiation results from the combined regulation of multiple hormones. In addition, several candidate genes associated with phytohormone biosynthesis and signal transduction pathways were identified, including AUX1, GH3, AHP, B-ARR, PP2C, etc., which provided candidate genes for the following hormone-related gene overexpression and knockout experiments. These findings provide insights into the molecular genetic control of seedling height growth of P. yunnanensis. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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19 pages, 6240 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Salt-Tolerance-Associated NAC Family Genes in Cyclocarya paliurus

by Ziwei Yang, Yin An, Qian Ye, Nannan Zhang, Xin Liu, Fayin He, Yue Zeng, Ming Tang, Zhengting Yang and Kun Li

Forests 2024, 15(3), 479; https://doi.org/10.3390/f15030479 - 4 Mar 2024

Cited by 2 | Viewed by 1674

Abstract

Soil salinity affects approximately 20% of the world’s arable land, presenting a significant challenge for studying the mechanisms by which plants adapt to saline environments. Cyclocarya paliurus, an invaluable research model due to its ecological and medicinal significance, is primarily concentrated in [...] Read more.

Soil salinity affects approximately 20% of the world’s arable land, presenting a significant challenge for studying the mechanisms by which plants adapt to saline environments. Cyclocarya paliurus, an invaluable research model due to its ecological and medicinal significance, is primarily concentrated in central and southern China. Nevertheless, Cyclocarya paliurus faces challenges from environmental factors such as soil salinization, which adversely impacts its growth, subsequently affecting the yield and quality of its bioactive compounds. The NAC gene family, a critical group of plant-specific transcription factors, plays pivotal roles in responding to abiotic stresses. However, there has not yet been any studies on NAC genes under salt stress in Cyclocarya paliurus. In this study, we identified 132 NAC genes within the Cyclocarya paliurus genome. Our analysis of the conserved structures and gene organization revealed a high degree of conservation in the proteins of the CpNAC gene family. Cis-element analysis unveiled the participation of these genes in a variety of biological processes, including light responses, phytohormone responses, cell cycle responses, and abiotic stress responses. Under salt stress conditions, the expression of 35 CpNAC genes changed significantly, indicating a response to salt treatment. Furthermore, we provided additional evidence for the identification of the NAC gene family and revealed their potential positive regulatory role in signal transduction by conducting a transcriptional activation activity analysis of CpNAC132(D) and CpNAC040, which are homologous to Arabidopsis thaliana NAC062/91 and NAC103, respectively. This research not only advances our comprehension of the salt stress adaptation in Cyclocarya paliurus but also provides robust support for future investigations into plant responses to environmental stress and the cultivation of salt-tolerant crops. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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18 pages, 3076 KiB

Open AccessArticle

Insights into the Root Sprouts of Toona fargesii in a Natural Forest: From the Morphology, Physiology, and Transcriptome Levels

by Qiangqiang Cheng, Jikai Ma, Chunce Guo, Qiuwei Zhong, Wanwen Yu, Ting Jia and Lu Zhang

Forests 2024, 15(2), 335; https://doi.org/10.3390/f15020335 - 8 Feb 2024

Cited by 3 | Viewed by 1615

Abstract

Toona fargesii (T. fargesii) is a deciduous tree of the Meliaceae family which is utilized for high-value timber. Interestingly, root sprouting is a typical reproductive pattern in T. fargesii. Nevertheless, the genetics underlying this phenomenon are still unclear. Here, three [...] Read more.

Toona fargesii (T. fargesii) is a deciduous tree of the Meliaceae family which is utilized for high-value timber. Interestingly, root sprouting is a typical reproductive pattern in T. fargesii. Nevertheless, the genetics underlying this phenomenon are still unclear. Here, three type of roots of T. fargesii were used for histological observation, plant endogenous hormone determination, non-structural carbohydrate (NSC) determination, and sequencing using the Illumina next-generation and PacBio SMRT platforms. Our results indicated that root sprouts originated from cork cambiums. Furthermore, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellic acid 3 (GA3), and abscisic acid (ABA) content was significantly increased, while soluble sugar content was significantly decreased in the root sprouts. In addition, transcriptomic analysis suggested a total of 36.19 G of raw data from which 210 differentially expressed genes (DEGs) of were identified in RS vs. SR. Of these, the candidate DEGs were largely enriched in the citrate cycle, gluconeogenesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. We therefore speculated that the accumulation of cytokinin and auxin might be induced by ATP-binding cassette-B 19 (ABCB19) and ABCG14, which were necessary for root sprouting. Additionally, transcription factors SQUAMOSA promoter binding protein-like 18 (SPL18) and NAM, ATAF1/2, and CUC2-14 (NAC14) were found in response to environmental water and epigenetic modification in RS. Overall, this study was to unravel the physiological and transcriptomic levels of the development of root sprouting in T. fargesii. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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16 pages, 8888 KiB

Open AccessArticle

Comparative Chloroplast Genome Analyses of Six Hemlock Trees in East Asia: Insights into Their Genomic Characterization and Phylogenetic Relationship

by Lin Chen, Xin Liu, Zhibei Wang, Xi Wu, Kaiyue Hong and Chunping Xie

Forests 2023, 14(11), 2136; https://doi.org/10.3390/f14112136 - 26 Oct 2023

Cited by 5 | Viewed by 1780

Abstract

Hemlocks (Pinaceae: Tsuga) are widely distributed in North America and East Asia, forming a reticulate evolutionary structure in East Asia with significant ecological importance. To clarify the chloroplast genome characteristics and phylogenetic relationships among Tsuga species, we analyzed the chloroplast genomes of [...] Read more.

Hemlocks (Pinaceae: Tsuga) are widely distributed in North America and East Asia, forming a reticulate evolutionary structure in East Asia with significant ecological importance. To clarify the chloroplast genome characteristics and phylogenetic relationships among Tsuga species, we analyzed the chloroplast genomes of T. chinensis var. tchekiangensis, T. chinensis, T. diversifolia, T. dumosa, T. forrestii, and T. sieboldii, performing associated phylogenetic analyses. The results reveal that the chloroplast genome lengths among the six Tsuga species vary from 120,520 to 121,010 bp, encompassing about 108 to 112 genes, including 35/32 tRNA genes and 4 rRNA genes. A codon usage analysis highlighted a preference for A/U-ending codons, and all six nucleotide types have A/T bases and a prevalence of mononucleotides. Notably, all Tsuga species exhibit inverted repeat (IR) contractions and possess unique hexanucleotides absent in the other species of Pinaceae, potentially making them more susceptible to gene recombination or rearrangement during evolution. While most variations are observed in non-coding regions, particularly in intergenic fragments, substantial variation sites are also present within the genes. The phylogenetic tree, constructed using chloroplast genomes, substantiates the sister taxa relationship between Tsuga and Nothotsuga. Furthermore, it confirms that T. chinensis var. tchekiangensis exhibits a closer relationship with T. forrestii than with T. chinensis. These findings not only provide partial evidence that T. chinensis may not constitute a monophyletic species but also underscore the necessity of reevaluating the taxonomic status of T. chinensis var. tchekiangensis. In addition, while the RSCU cluster analysis is basically consistent with the phylogenetic analysis, it also highlights a distinct differentiation between Nothotsuga and Tsuga. This study not only provides molecular-level phylogenetic classification evidence of Pinaceous genera via chloroplast genome analyses but also offers compelling evidence for further exploring the relationships and species delimitation among the hemlocks of East Asia. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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17 pages, 5882 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of the DGAT Gene Family in Lindera glauca and Expression Analysis during Fruit Development Stages

by Xue Bai, Yongyi Yang, Lun Xie, Qingqing Li and Biao Xiong

Forests 2023, 14(8), 1633; https://doi.org/10.3390/f14081633 - 13 Aug 2023

Viewed by 1718

Abstract

Diacylglycerol acyltransferase (DGAT) is a vital and sole rate-limiting enzyme involved in triacylglycerol synthesis. Identifying DGAT genes in Lindera glauca is essential for studying lipid metabolism pathways and developing novel oil crops with enhanced value. In the study reported in this paper, 15 [...] Read more.

Diacylglycerol acyltransferase (DGAT) is a vital and sole rate-limiting enzyme involved in triacylglycerol synthesis. Identifying DGAT genes in Lindera glauca is essential for studying lipid metabolism pathways and developing novel oil crops with enhanced value. In the study reported in this paper, 15 LgDGAT family genes were first obtained from the L. glauca genome via bioinformatics analysis. We comprehensively analyzed their chromosome distribution, gene structure, subcellular localization, promoter prediction, phylogenetic relationships, tissue-specific expression, and expression patterns during different stages of fruit development. Our findings revealed that LgDGATs can be classified into DGAT1, DGAT2, DGAT3, and WSD (wax ester synthase/acyl-CoA: diacylglycerol acyltransferase) subfamilies distributed across chromosome 3, 5, 6, 8 and 11. LgDGATs’ promoter region showed abundant elements linked to the light response and plant hormone response. Forms of LgDGAT1, LgDGAT2, and LgDGAT3 were primarily expressed in the early and late phases of fruit development, indicating their potential function in the growth and development of L. glauca, particularly in oil accumulation. Conversely, LgWSDs exhibited predominant expression in stems and leaves. This paper elucidates the gene structure and expression patterns of LgDGATs, providing a theoretical foundation for understanding the functionality of DGAT genes in Lindera species. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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19 pages, 37786 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of B3 Transcription Factor Genes in Prunus armeniaca

by Xiaodan Shi, Wanwen Yu, Lin Wang, Han Zhao, Jingjing Hu, Tana Wuyun and Huimin Liu

Forests 2023, 14(8), 1523; https://doi.org/10.3390/f14081523 - 26 Jul 2023

Cited by 2 | Viewed by 1944

Abstract

The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 [...] Read more.

The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 B3 genes were identified from the apricot genome. The apricot B3 superfamily can be divided into five subfamilies, i.e., REM, ARF, ABI3, RAV, and HSI, and genes in the same subfamily have similar structures. The distribution of B3 genes on chromosomes presents a clustering phenomenon. Tandem duplication is the main mode of apricot B3 family expansion, and gene duplication mainly occurs in the REM and ARF subfamilies. Many B3 genes originated from a common ancestor of Arabidopsis and apricot before lineage divergence, and ancestor genes expanded fewer times in apricot than in Arabidopsis. Gene ontology analysis showed that apricot B3 genes were closely related to vernalization, flower development, and shoot system development. PaABI3-1 and PaABI3-2 might play a positive regulation role in the transcription of PaOleosin, which encodes a lipid body protein. This study lays a foundation for the further study of the B3 superfamily function in apricot, especially the specific functions of the ABI3 subfamily in apricot kernel oil storage. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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13 pages, 3200 KiB

Open AccessArticle

Functional Characterization of a New Salt Stress Response Gene, PeCBL4, in Populus euphratica Oliv

by Meiqiao Qu, Qi Sun, Ningning Chen, Zhuoyan Chen, Hechen Zhang, Fuling Lv and Yi An

Forests 2023, 14(7), 1504; https://doi.org/10.3390/f14071504 - 23 Jul 2023

Cited by 1 | Viewed by 1561

Abstract

Populus euphratica is a typical stress-resistant tree species that provides valuable natural genetic resources for breeding salt-tolerant plants. The calcineurin B-like (CBL)-interacting protein kinase (CIPK) network plays an important role in regulating plant responses to abiotic stresses. The aim of this study was [...] Read more.

Populus euphratica is a typical stress-resistant tree species that provides valuable natural genetic resources for breeding salt-tolerant plants. The calcineurin B-like (CBL)-interacting protein kinase (CIPK) network plays an important role in regulating plant responses to abiotic stresses. The aim of this study was to characterize the function of a new CBL member, PeCBL4, in response to abiotic stresses. PeCBL4 was cloned, and sequence analysis was performed. The subcellular localization of PeCBL4 was determined using the fusion expression vector of GFP. Yeast two-hybrid assays and bimolecular fluorescence complementation were performed to identify PeCIPK members that interacted with PeCBL4. PeCBL4 was then transformed into the corresponding Arabidopsis thaliana mutants. Na⁺ and K⁺ content as well as their net fluxes were determined under high salt stress and low K⁺ stress. Phylogenetic tree analysis showed that PeCBL4 was clustered together with PtCBL4 and belonged to the same subgroup as AtCBL4. Subcellular localization indicated that PeCBL4 was expressed on the plasma membrane. Yeast two-hybrid assays and bimolecular fluorescence complementation showed that PeCBL4 interacted with PeCIPK24 and PeCIPK26. In addition, under high salt stress, the Na⁺ efflux capacities of seedlings decreased in sos3 mutants, and transgenic plants of PeCBL4 enhanced efflux capacities. In addition, the overexpression of PeCBL4 negatively influenced the influx capacity of K⁺. PeCBL4 interacts with PeCIPK24 and PeCIPK26 and regulates Na⁺/K⁺ balance under low K⁺ and high salt stress. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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12 pages, 1753 KiB

Open AccessArticle

Stilbene Content and Expression of Stilbene Synthase Genes in Korean Pine Pinus koraiensis Siebold & Zucc

by Andrey R. Suprun, Alexandra S. Dubrovina, Valeria P. Grigorchuk and Konstantin V. Kiselev

Forests 2023, 14(6), 1239; https://doi.org/10.3390/f14061239 - 15 Jun 2023

Cited by 3 | Viewed by 2177

Abstract

Stilbenes are a large group of plant phenolic compounds that have a wide range of biologically active properties, such as antioxidant, immunomodulatory, anti-inflammatory, and anti-angiogenic effects. In plants, stilbenes are involved in the defense against environmental stresses, including fungal infections and insect attacks. [...] Read more.

Stilbenes are a large group of plant phenolic compounds that have a wide range of biologically active properties, such as antioxidant, immunomodulatory, anti-inflammatory, and anti-angiogenic effects. In plants, stilbenes are involved in the defense against environmental stresses, including fungal infections and insect attacks. The biosynthesis of stilbenes is well described for those plant species where resveratrol and its derivatives are the predominant stilbenes. However, there is little information on stilbene biosynthesis in the Pinaceae family, although the highest content of stilbenes was found in plants of this family. In this study, seasonal variations in stilbene compositions and contents in different parts of Pinus koraiensis was described (needles, bark, wood, young branches, and strobiles). HPLC-ESI-MS analysis showed the presence of seven stilbenes in P. koraiensis: t-astringin; t-piceid; cis-piceid; t-isorapontin; t-pinostilbenoside; t-resveratrol; and t-pinostilbene. Glycosylated and methylated forms of stilbenes, such as t-astringin, t-piceid, and t-pinostilbenoside, prevailed over other stilbenoids. The highest content of stilbenes was detected in the bark collected in spring and winter (up to 54.8 mg/g dry weight). The complete protein-coding sequences of three stilbene synthase genes, PkSTS1, PkSTS2, and PkSTS3, were obtained from the RNA isolated from the P. koraiensis needles. The expression of the PkSTS1, PkSTS2, and PkSTS3 genes was analyzed using real-time PCR and frequency analysis of cloned RT-PCR products in the needles of P. koraiensis collected in different seasons. Thus, we first analyzed stilbene biosynthesis in the different organs of pine P. koraiensis and PkSTS expression depending on the year seasons. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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13 pages, 6644 KiB

Open AccessArticle

Genome-Wide Analysis, Identification, and Characterization of the PFK Gene Family Members of Populus deltoides

by Tae-Lim Kim, Michael Immanuel Jesse Denison, Hyemin Lim, Hoyong Chung and Changyoung Oh

Forests 2023, 14(6), 1104; https://doi.org/10.3390/f14061104 - 26 May 2023

Cited by 3 | Viewed by 1946

Abstract

Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. [...] Read more.

Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. deltoides genome, including their gene structure, conserved domains, evolutionary relationships, and expression patterns. Genome-wide analysis of the poplar genome identified 11 genes belonging to PdPFK and 6 genes belonging to PdPFP. Phylogenetic, gene structure, and motif analyses revealed two main categories of PFK genes: PFK with eleven genes and PFP with six genes. Quantitative PCR (qPCR) analysis demonstrated that all 17 phosphofructokinase genes were induced in various tissues and developmental stages of P. deltoides. PFPs were strongly expressed throughout P. deltoides’ growth and development, notably in the roots, according to the transcript analysis. This genome-wide analysis provides insights into PFK and PFP genes and establishes a foundation for future investigations into the role of genes in P. deltoids. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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Review

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14 pages, 2464 KiB

Open AccessReview

Progress in Research on Terpenoid Biosynthesis and Terpene Synthases of Lauraceae Species

by Chenyi Xie, Junhao Gu and Shanshan Zhu

Forests 2024, 15(10), 1731; https://doi.org/10.3390/f15101731 - 29 Sep 2024

Cited by 2 | Viewed by 1918

Abstract

Lauraceae, an important family of Angiospermae, comprises over 2500 species widely distributed in tropical and subtropical evergreen broad-leaved forests. This family is renowned for its rich resource of terpenoids, particularly monoterpenes, sesquiterpenes, and diterpenes. These compounds not only impart specific scents to Lauraceae [...] Read more.

Lauraceae, an important family of Angiospermae, comprises over 2500 species widely distributed in tropical and subtropical evergreen broad-leaved forests. This family is renowned for its rich resource of terpenoids, particularly monoterpenes, sesquiterpenes, and diterpenes. These compounds not only impart specific scents to Lauraceae species but also play crucial roles in plant growth, development, and environmental adaptation. These compounds also possess extensive bioactivities, such as antioxidant, antibacterial, anti-inflammatory, and neuroprotective effects, making them valuable in the fields of perfumery, cosmetics, food, and medicine, and thus holding significant economic value. Recent advancements in high-throughput technologies, especially genomics, transcriptomics, and metabolomics, have significantly advanced our knowledge of the chemical constituents and biosynthetic pathways of terpenoids in Lauraceae species. Such progress has also shed light on the diversity and functionality of the terpene synthases (TPSs) gene family, a key enzyme involved in terpenoid biosynthesis. This paper reviews the latest research findings on the biosynthetic pathways of terpenoids and their key enzyme-encoding gene families in Lauraceae plants. We also analyze the evolutionary patterns of TPS gene family members of four Lauraceae species at the whole-genome level and summarize their mechanisms of action in secondary metabolite synthesis. Furthermore, this paper highlights the current research challenges and proposes prospects, such as the complexity of gene families, the uncertainties in functional predictions, and unclear regulatory mechanisms. Our objective is to provide scientific foundations for the in-depth analysis of terpenoid biosynthesis mechanisms and the development and utilization of natural products in Lauraceae plants. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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22 pages, 1886 KiB

Open AccessReview

Multi-Omics Techniques in Genetic Studies and Breeding of Forest Plants

by Mingcheng Wang, Rui Li and Qi Zhao

Forests 2023, 14(6), 1196; https://doi.org/10.3390/f14061196 - 9 Jun 2023

Cited by 10 | Viewed by 3337

Abstract

In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted [...] Read more.

In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration combines the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies on forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs. Full article

(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)

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