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Genomic Studies of Plant-Environment Interactions

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

Deadline for manuscript submissions: closed (15 July 2021) | Viewed by 27721

Special Issue Editor

Special Issue Information

Dear Colleagues,

The growth and development of plants are strongly affected by the abiotic and biotic environments. Plants have developed multiple levels of responses to environmental challenges. Recent advancements in genome biology have unveiled the underlying mechanisms of genetic and epigenetic regulations of plant-environment interactions. This Special Issue explores the current conceptual and technological breakthrough in this aspect.

Prof. Dr. Hon-Ming Lam
Guest Editor

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Keywords

  • Plant defense
  • Plant immunity
  • Plant-microbe interaction
  • Plant signal transduction
  • Resistance genes
  • Signaling crosstalk
  • Abiotic stress tolerance
  • Genomics
  • Epigenomics
  • Gene regulations

Published Papers (8 papers)

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Editorial

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3 pages, 181 KiB  
Editorial
Genomic Studies of Plant-Environment Interactions
by Man-Wah Li and Hon-Ming Lam
Int. J. Mol. Sci. 2022, 23(11), 5871; https://doi.org/10.3390/ijms23115871 - 24 May 2022
Cited by 2 | Viewed by 1144
Abstract
Plants have been evolving for millions of years to survive in their fast-changing environments, by promoting beneficial interactions with other organisms or taking advantage of new conditions in the physical environment, while finding ways to repel pathogens and pests or tolerate unfavorable conditions [...] Read more.
Plants have been evolving for millions of years to survive in their fast-changing environments, by promoting beneficial interactions with other organisms or taking advantage of new conditions in the physical environment, while finding ways to repel pathogens and pests or tolerate unfavorable conditions [...] Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)

Research

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22 pages, 9891 KiB  
Article
Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire
by Mojtaba Mohammadi, Eric A. Smith, Michael E. Stanghellini and Rakesh Kaundal
Int. J. Mol. Sci. 2021, 22(16), 9002; https://doi.org/10.3390/ijms22169002 - 20 Aug 2021
Cited by 3 | Viewed by 2425
Abstract
Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host [...] Read more.
Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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18 pages, 4999 KiB  
Article
Systematic Genome-Wide Study and Expression Analysis of SWEET Gene Family: Sugar Transporter Family Contributes to Biotic and Abiotic Stimuli in Watermelon
by Changqing Xuan, Guangpu Lan, Fengfei Si, Zhilong Zeng, Chunxia Wang, Vivek Yadav, Chunhua Wei and Xian Zhang
Int. J. Mol. Sci. 2021, 22(16), 8407; https://doi.org/10.3390/ijms22168407 - 05 Aug 2021
Cited by 20 | Viewed by 3039
Abstract
The SWEET (Sugars Will Eventually be Exported Transporter) proteins are a novel family of sugar transporters that play key roles in sugar efflux, signal transduction, plant growth and development, plant–pathogen interactions, and stress tolerance. In this study, 22 ClaSWEET genes were identified in [...] Read more.
The SWEET (Sugars Will Eventually be Exported Transporter) proteins are a novel family of sugar transporters that play key roles in sugar efflux, signal transduction, plant growth and development, plant–pathogen interactions, and stress tolerance. In this study, 22 ClaSWEET genes were identified in Citrullus lanatus (Thunb.) through homology searches and classified into four groups by phylogenetic analysis. The genes with similar structures, conserved domains, and motifs were clustered into the same groups. Further analysis of the gene promoter regions uncovered various growth, development, and biotic and abiotic stress responsive cis-regulatory elements. Tissue-specific analysis showed most of the genes were highly expressed in male flowers and the roots of cultivated varieties and wild cultivars. In addition, qRT-PCR results further imply that ClaSWEET proteins might be involved in resistance to Fusarium oxysporum infection. Moreover, a significantly higher expression level of these genes under various abiotic stresses suggests its multifaceted role in mediating plant responses to drought, salt, and low-temperature stress. The genome-wide characterization and phylogenetic analysis of ClaSWEET genes, together with the expression patterns in different tissues and stimuli, lays a solid foundation for future research into their molecular function in watermelon developmental processes and responses to biotic and abiotic stresses. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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20 pages, 2777 KiB  
Article
Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions
by Ali Raza, Wei Su, Ang Gao, Sundas Saher Mehmood, Muhammad Azhar Hussain, Wenlong Nie, Yan Lv, Xiling Zou and Xuekun Zhang
Int. J. Mol. Sci. 2021, 22(8), 4281; https://doi.org/10.3390/ijms22084281 - 20 Apr 2021
Cited by 73 | Viewed by 8526
Abstract
Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide [...] Read more.
Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (H2O2) to water (H2O) and reduce the ROS levels to shelter the cells’ death. So far, the CAT gene family has not been reported in rapeseed (Brassica napus L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the rapeseed genome. The current study identified 14 BnCAT genes in the rapeseed genome. Based on phylogenetic and synteny analysis, the BnCATs belong to four groups (Groups I–IV). A gene structure and conserved motif analysis showed that Group I, Group II, and Group IV possess almost the same intron/exon pattern, and an equal number of motifs, while Group III contains diverse structures and contain 15 motifs. By analyzing the cis-elements in the promoters, we identified five hormone-correlated responsive elements and four stress-related responsive elements. Further, six putative bna-miRNAs were also identified, targeting three genes (BnCAT4, BnCAT6, and BnCAT8). Gene ontology (GO) enrichment analysis showed that the BnCAT genes were largely related to cellular organelles, ROS response, stimulus response, stress response, and antioxidant enzymes. Almost 10 BnCAT genes showed higher expression levels in different tissues, i.e., root, leaf, stem, and silique. The expression analysis showed that BnCAT1–BnCAT3 and BnCAT11–BnCAT13 were significantly upregulated by cold, salinity, abscisic acid (ABA), and gibberellic acid (GA) treatment, but not by drought and methyl jasmonate (MeJA). Notably, most of the genes were upregulated by waterlogging stress, except BnCAT6, BnCAT9, and BnCAT10. Our results opened new windows for future investigations and provided insights into the CAT family genes in rapeseed. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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18 pages, 16518 KiB  
Article
A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils
by Juan Liu, Xiangwei He, Jingya Sun and Yuchao Ma
Int. J. Mol. Sci. 2021, 22(7), 3438; https://doi.org/10.3390/ijms22073438 - 26 Mar 2021
Cited by 13 | Viewed by 2417
Abstract
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient [...] Read more.
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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19 pages, 22464 KiB  
Article
Genome Wide Analysis of U-Box E3 Ubiquitin Ligases in Wheat (Triticum aestivum L.)
by Dae Yeon Kim, Yong Jin Lee, Min Jeong Hong, Jae Ho Kim and Yong Weon Seo
Int. J. Mol. Sci. 2021, 22(5), 2699; https://doi.org/10.3390/ijms22052699 - 07 Mar 2021
Cited by 20 | Viewed by 3110
Abstract
U-box E3 ligase genes play specific roles in protein degradation by post-translational modification in plant signaling pathways, developmental stages, and stress responses; however, little is known about U-box E3 genes in wheat. We identified 213 U-box E3 genes in wheat based on U-box [...] Read more.
U-box E3 ligase genes play specific roles in protein degradation by post-translational modification in plant signaling pathways, developmental stages, and stress responses; however, little is known about U-box E3 genes in wheat. We identified 213 U-box E3 genes in wheat based on U-box and other functional domains in their genome sequences. The U-box E3 genes were distributed among 21 chromosomes and most showed high sequence homology with homoeologous U-box E3 genes. Synteny analysis of wheat U-box E3 genes was conducted with other plant species such as Brachypodium distachyon, barley, rice, Triricum uratu, and Aegilops tauschii. A total of 209 RNA-seq samples representing 22 tissue types, from grain, root, leaf, and spike samples across multiple time points, were analyzed for clustering of U-box E3 gene expression during developmental stages, and the genes responded differently in various tissues and developmental stages. In addition, expression analysis of U-box E3 genes under abiotic stress, including drought, heat, and both heat and drought, and cold conditions, was conducted to provide information on U-box E3 gene expression under specific stress conditions. This analysis of U-box E3 genes could provide valuable information to elucidate biological functions for a better understanding of U-box E3 genes in wheat. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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20 pages, 3544 KiB  
Article
Genome-Wide Identification and Expression Analysis of OsbZIP09 Target Genes in Rice Reveal Its Mechanism of Controlling Seed Germination
by Cheng-Chao Zhu, Chu-Xin Wang, Chen-Ya Lu, Jin-Dong Wang, Yu Zhou, Min Xiong, Chang-Quan Zhang, Qiao-Quan Liu and Qian-Feng Li
Int. J. Mol. Sci. 2021, 22(4), 1661; https://doi.org/10.3390/ijms22041661 - 07 Feb 2021
Cited by 10 | Viewed by 3321
Abstract
Seed dormancy and germination are key events in plant development and are critical for crop production, and defects in seed germination or the inappropriate release of seed dormancy cause substantial losses in crop yields. Rice is the staple food for more than half [...] Read more.
Seed dormancy and germination are key events in plant development and are critical for crop production, and defects in seed germination or the inappropriate release of seed dormancy cause substantial losses in crop yields. Rice is the staple food for more than half of the world’s population, and preharvest sprouting (PHS) is one of the most severe problems in rice production, due to a low level of seed dormancy, especially under warm and damp conditions. Therefore, PHS leads to yield loss and a decrease in rice quality and vitality. We reveal that mutation of OsbZIP09 inhibited rice PHS. Analysis of the expression of OsbZIP09 and its encoded protein sequence and structure indicated that OsbZIP09 is a typical bZIP transcription factor that contains conserved bZIP domains, and its expression is induced by ABA. Moreover, RNA sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analyses were performed and 52 key direct targets of OsbZIP09 were identified, including OsLOX2 and Late Embryogenesis Abundant (LEA) family genes, which are involved in controlling seed germination. Most of these key targets showed consistent changes in expression in response to abscisic acid (ABA) treatment and OsbZIP09 mutation. The data characterize a number of key target genes that are directly regulated by OsbZIP09 and contribute to revealing the molecular mechanism that underlies how OsbZIP09 controls rice seed germination. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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Review

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12 pages, 1473 KiB  
Review
The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants
by Lee-Ann Niekerk, Mogamat Fahiem Carelse, Olalekan Olanrewaju Bakare, Vuyo Mavumengwana, Marshall Keyster and Arun Gokul
Int. J. Mol. Sci. 2021, 22(13), 7046; https://doi.org/10.3390/ijms22137046 - 30 Jun 2021
Cited by 12 | Viewed by 2693
Abstract
Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort [...] Read more.
Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance. Full article
(This article belongs to the Special Issue Genomic Studies of Plant-Environment Interactions)
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