Applications of Bioinformatics in Plant Resources and Omics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 36315

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Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM La Mayora-CSIC-UMA), Avenida Dr. Wienberg, s/n. Algarrobo-Costa, 29750 Málaga, Spain
Interests: bioinformatics; plant genomics; transcriptomics; annotation; bioinformatics tools; olive; avocado; mango
Special Issues, Collections and Topics in MDPI journals

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Department of Molecular Biology and Biochemistry, University of Malaga, 29071 Malaga, Spain
Interests: transcriptomics; next generation sequencing; genomics; bioinformatics and computational biology; gene expression; bioinformatics; sequencing; DNA computational biology; DNA sequencing; plant abiotic stress; pollen allergens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advances in sequencing technologies and genome assembly methods that do not require genetic maps to generate chromosome-scale genome references are generating a plethora of genome sequences in plants, especially for non-model species. Today, projects to sequence thousands of plant transcriptomes and genomes are in progress, and many bioinformatics tools have been developed and applied for omics plant research. These advances are allowing us to access a great number of useful resources and bioinformatics tools to study plants, in some cases in species which had few or even no omics data before. This Special Issue of Plants aims to highlight omics resources produced for plants, such as genomes, transcriptomes, gene expression data, gene or genome annotations, metabolomes, proteomes, epigenomes, and metagenomes of microorganisms interacting with plants, and bioinformatics tools used or developed to generate these resources, such as analysis tools, automated pipelines, databases or web tools.

Dr. Noe Fernandez-Pozo
Prof. Dr. M. Gonzalo Claros
Guest Editors

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Keywords

  • bioinformatics tools
  • databases
  • genomics
  • DNA-seq
  • RNA-seq
  • polymorphisms
  • biomarkers
  • transcriptomics
  • metabolomics
  • metagenomics
  • proteomics
  • epigenetics
  • annotations
  • resources
  • Iso-seq
  • alternative splicing
  • functional analysis

Published Papers (22 papers)

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15 pages, 4256 KiB  
Article
Integrated Transcriptome and Proteome Analysis Reveals That Cell Wall Activity Affects Phelipanche aegyptiaca Parasitism
by Meixiu Chen, Lu Zhang, Zhaoqun Yao, Xiaolei Cao, Qianqian Ma, Siyu Chen, Xuekun Zhang and Sifeng Zhao
Plants 2024, 13(6), 869; https://doi.org/10.3390/plants13060869 - 18 Mar 2024
Viewed by 485
Abstract
Phelipanche aegyptiaca can infect many crops, causing large agricultural production losses. It is important to study the parasitism mechanism of P. aegyptiaca to control its harm. In this experiment, the P. aegyptiaca HY13M and TE9M from Tacheng Prefecture and Hami City in Xinjiang, [...] Read more.
Phelipanche aegyptiaca can infect many crops, causing large agricultural production losses. It is important to study the parasitism mechanism of P. aegyptiaca to control its harm. In this experiment, the P. aegyptiaca HY13M and TE9M from Tacheng Prefecture and Hami City in Xinjiang, respectively, were used to analyze the parasitical mechanism of P. aegyptiaca by means of transcriptome and proteome analyses. The parasitic capacity of TE9M was significantly stronger than that of HY13M in Citrullus lanatus. The results showed that the DEGs and DEPs were prominently enriched in the cell wall metabolism pathways, including “cell wall organization or biogenesis”, “cell wall organization”, and “cell wall”. Moreover, the functions of the pectinesterase enzyme gene (TR138070_c0_g), which is involved in the cell wall metabolism of P. aegyptiaca in its parasitism, were studied by means HIGS. The number and weight of P. aegyptiaca were significantly reduced when TR138070_c0_g1, which encodes a cell-wall-degrading protease, was silenced, indicating that it positively regulates P. aegyptiaca parasitism. Thus, these results suggest that the cell wall metabolism pathway is involved in P. aegyptiaca differentiation of the parasitic ability and that the TR138070_c0_g1 gene plays an important role in P. aegyptiaca’s parasitism. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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19 pages, 2668 KiB  
Article
Genotype-Dependent Response of Root Microbiota and Leaf Metabolism in Olive Seedlings Subjected to Drought Stress
by Rahma Azri, Myriam Lamine, Asma Bensalem-Fnayou, Zohra Hamdi, Ahmed Mliki, Juan Manuel Ruiz-Lozano and Ricardo Aroca
Plants 2024, 13(6), 857; https://doi.org/10.3390/plants13060857 - 15 Mar 2024
Viewed by 715
Abstract
Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in [...] Read more.
Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in maintaining the host homeostasis remains insufficiently investigated. In this study, we aimed to assess the specificity of the foliar metabolic response of contrasting olive genotypes to microbial inoculation with wet-adapted consortia of plant-growth-promoting rhizobacteria (PGPR), to see if previously inoculated plants with indigenous or exogenous microbes would display any change in their leaf metabolome once being subjected to drought stress. Two Tunisian elite varieties, Chetoui (drought-sensitive) and Chemleli (drought-tolerant), were tested under controlled and stressed conditions. Leaf samples were analyzed by gas chromatography–mass spectrometry (GC-TOFMS) to identify untargeted metabolites. Root and soil samples were used to extract microbial genomic DNA destined for bacterial community profiling using 16S rRNA amplicon sequencing. Respectively, the score plot analysis, cluster analysis, heat map, Venn diagrams, and Krona charts were applied to metabolic and microbial data. Results demonstrated dynamic changes in the leaf metabolome of the Chetoui variety in both stress and inoculation conditions. Under the optimum state, the PGPR consortia induced noteworthy alterations in metabolic patterns of the sensitive variety, aligning with the phytochemistry observed in drought-tolerant cultivars. These variations involved fatty acids, tocopherols, phenols, methoxyphenols, stilbenoids, triterpenes, and sugars. On the other hand, the Chemleli variety displaying comparable metabolic profiles appeared unaffected by stress and inoculation probably owing to its tolerance capacity. The distribution of microbial species among treatments was distinctly uneven. The tested seedlings followed variety-specific strategies in selecting beneficial soil bacteria to alleviate stress. A highly abundant species of the wet-adapted inoculum was detected only under optimum conditions for both cultivars, which makes the moisture history of the plant genotype a selective driver shaping microbial community and thereby a useful tool to predict microbial activity in large ecosystems. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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30 pages, 5989 KiB  
Article
Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae
by Mouna Ghorbel, Ikram Zribi, Najla Haddaji, Arif Jamal Siddiqui, Nouha Bouali and Faiçal Brini
Plants 2024, 13(1), 11; https://doi.org/10.3390/plants13010011 - 19 Dec 2023
Viewed by 1073
Abstract
Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell [...] Read more.
Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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14 pages, 3723 KiB  
Article
Genome-Wide Identification and Analysis of the WNK Kinase Gene Family in Upland Cotton
by Qi Zhang, Caidie Zhang, Zhenyuan Pan, Hairong Lin, Zhibo Li, Xinhe Hou, Jinshan Liu, Xinhui Nie and Yuanlong Wu
Plants 2023, 12(23), 4036; https://doi.org/10.3390/plants12234036 - 30 Nov 2023
Cited by 1 | Viewed by 860
Abstract
With-No-Lysine (WNK) kinases are a subfamily of serine/threonine protein kinases. WNKs are involved in plant abiotic stress response and circadian rhythms. However, members of the WNK subfamily and their responses to abiotic and biotic stresses in Gossypium hirsutum have not been reported. In [...] Read more.
With-No-Lysine (WNK) kinases are a subfamily of serine/threonine protein kinases. WNKs are involved in plant abiotic stress response and circadian rhythms. However, members of the WNK subfamily and their responses to abiotic and biotic stresses in Gossypium hirsutum have not been reported. In this study, 26 GhWNKs were identified in G. hirsutum. The gene structure, conserved motifs, and upstream open reading frames (uORFs) of GhWNKs were identified. Moreover, GhWNKs regulation is predicted to be regulated by cis-acting elements, such as ABA responsive element (ABRE), MBS, and MYC. Furthermore, transcription factors including MIKC_MADS, C2H2, TALE, bZIP, Dof, MYB, bHLH, and HD-ZIP are projected to play a regulatory role in GhWNKs. The expression patterns of GhWNKs under normal conditions and biotic and abiotic stresses were evaluated, and their expression was found to vary. The expression patterns of several GhWNKs were induced by infiltration with Verticillium dahliae, suggesting that several GhWNKs may play important roles in the response of cotton to V. dahliae. Interestingly, a homoeologous expression bias within the GhWNKs was uncovered in upland cotton. Homoeologous expression bias within GhWNKs provides a framework to assist researchers and breeders in developing strategies to improve cotton traits by manipulating individual or multiple homeologs. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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25 pages, 11915 KiB  
Article
Changes in the Metabolome and Nutritional Quality of Pulp from Three Types of Korla Fragrant Pears with Different Appearances as Revealed by Widely Targeted Metabolomics
by Wei Jiang, Pan Yan, Qiangqing Zheng, Zhendong Wang, Qiling Chen and Yi Wang
Plants 2023, 12(23), 3981; https://doi.org/10.3390/plants12233981 - 27 Nov 2023
Viewed by 800
Abstract
Korla fragrant pear (Pyrus sinkiangensis Yü) fruits have a unique flavor and are rich in phenolic acids, flavonoids, amino acids, and other nutrients. At present, the molecular basis of the quality differences among Korla fragrant pear fruits with a convex calyx and [...] Read more.
Korla fragrant pear (Pyrus sinkiangensis Yü) fruits have a unique flavor and are rich in phenolic acids, flavonoids, amino acids, and other nutrients. At present, the molecular basis of the quality differences among Korla fragrant pear fruits with a convex calyx and rough skin (RS), calyx shedding (SD), and a convex calyx (CV) remains unknown. To analyze the main metabolic components of Korla fragrant pear fruits and compare the antioxidant activities of these three fruits with different qualities, we used nutrient composition analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS)-based widely targeted metabolomics approaches to analyze the changes in the quality characteristics of the pulp of these three Korla fragrant pear fruits with different appearances. The nutrient composition analysis showed that the fructose and glucose contents were not significantly different, and sucrose and vitamin C contents were significantly higher in SD fruits compared with CV and RS fruits. However, the levels of flavor substances such as titratable acids, total phenols, and total flavonoids were high in the pulp of RS fruits. The metabolomics results identified 1976 metabolites that were clustered into 12 categories, and phenolic acid and flavonoid metabolites were the most abundant. The differentially accumulated metabolites (DAMs) in the fruits with different appearances were screened by multivariate statistical methods, and a total of 595 DAMs were detected. The analysis identified 300 DAMs between the CV and SD fruits, 246 DAMs between the RS and CV fruits, and 405 DAMs between the RS and SD groups. SD fruits contained the most metabolites with a high relative content, especially phenolic acids, lipids, amino acids and derivatives, alkaloids, and organic acids. Compared with CV fruits, flavonoid metabolism was more active in RS fruits, which also had a higher content of flavonoids, whereas the fewest metabolites were found in CV fruits, which also displayed less flavonoid accumulation. KEGG pathway enrichment analysis revealed that the DAMs were mainly enriched in the metabolic pathways of flavone and flavonol biosynthesis, confirming that CV fruits have decreased flavone and flavonol biosynthesis and accumulate fewer flavonoids than RS fruits, which may explain the less bitter and astringent flavor of CV fruits. However, the flavonoid content in RS fruits was very high, which may be one of the reasons why RS fruits have a harder pulp and are less juicy, more slaggy, and less flavorful. Moreover, the analysis of the antioxidant activity showed that during fruit development and maturation, RS fruits had stronger antioxidant activity than SD and CV fruits. These results provide a theoretical basis for improving the fruit quality of Korla fragrant pears and the processing of pear pulp. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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15 pages, 2818 KiB  
Article
Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae
by Lydia Gramzow, Renu Sharma and Günter Theißen
Plants 2023, 12(18), 3281; https://doi.org/10.3390/plants12183281 - 15 Sep 2023
Viewed by 1034
Abstract
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. [...] Read more.
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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27 pages, 2970 KiB  
Article
Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors
by Amanda Bullones, Antonio Jesús Castro, Elena Lima-Cabello, Noe Fernandez-Pozo, Rocío Bautista, Juan de Dios Alché and Manuel Gonzalo Claros
Plants 2023, 12(16), 2894; https://doi.org/10.3390/plants12162894 - 08 Aug 2023
Cited by 2 | Viewed by 1398
Abstract
The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide [...] Read more.
The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide events underlying pollen hydration and growth in this species. To fill this gap, triplicate mRNA samples at 0, 1, 3, and 6 h of in vitro germination of olive cultivar Picual pollen were analysed by RNA-seq. A bioinformatics R workflow called RSeqFlow was developed contemplating the best practices described in the literature, covering from expression data filtering to differential expression and clustering, to finally propose hub genes. The resulting olive pollen transcriptome consisted of 22,418 reliable transcripts, where 5364 were differentially expressed, out of which 173 have no orthologue in plants and up to 3 of them might be pollen-specific transcription factors. Functional enrichment revealed a deep transcriptional reprogramming in mature olive pollen that is also dependent on protein stability and turnover to allow pollen tube emergence, with many hub genes related to heat shock proteins and F-box-containing proteins. Reprogramming extends to the first 3 h of growth, including processes consistent with studies performed in other plant species, such as global down-regulation of biosynthetic processes, vesicle/organelle trafficking and cytoskeleton remodelling. In the last stages, growth should be maintained from persistent transcripts. Mature pollen is equipped with transcripts to successfully cope with adverse environments, even though the in vitro growth seems to induce several stress responses. Finally, pollen-specific transcription factors were proposed as probable drivers of pollen germination in olive trees, which also shows an overall increased number of pollen-specific gene isoforms relative to other plants. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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20 pages, 1708 KiB  
Article
Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield
by Juan P. Mira, Anita Arenas-M, Daniel F. Calderini and Javier Canales
Plants 2023, 12(15), 2868; https://doi.org/10.3390/plants12152868 - 04 Aug 2023
Cited by 1 | Viewed by 1197
Abstract
This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed [...] Read more.
This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed genes across developmental stages. From this pool, 28,558 DEGs were found to exhibit significant temporal regulation in at least two different datasets and were enriched for processes integral to grain development such as carbohydrate metabolism and cell wall organization. Notably, 30% of the 241 known expansin genes showed differential expression during grain growth. Hierarchical clustering and expression level analysis revealed temporal regulation and distinct contributions of expansin subfamilies during the early stages of grain development. Further analysis using co-expression networks underscored the significance of expansin genes, revealing their substantial co-expression with genes involved in cell wall modification. Finally, qPCR validation and grain morphological analysis under field conditions indicated a significant negative correlation between the expression of select expansin genes, and grain size and weight. This study illuminates the potential role of expansin genes in wheat grain development and provides new avenues for targeted genetic improvements in wheat. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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22 pages, 14115 KiB  
Article
Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions
by Mouna Ghorbel, Ikram Zribi, Malek Besbes, Nouha Bouali and Faiçal Brini
Plants 2023, 12(14), 2720; https://doi.org/10.3390/plants12142720 - 21 Jul 2023
Cited by 5 | Viewed by 1104
Abstract
Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. In fact, the CAT enzyme modulates the hydrogen peroxide (H2O2) contents in cells by translating this toxic compound into water [...] Read more.
Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. In fact, the CAT enzyme modulates the hydrogen peroxide (H2O2) contents in cells by translating this toxic compound into water (H2O) and O2 to reduce reactive oxygen species (ROS) contents in cells. ROS are produced as a result of biotic and abiotic environmental stressors. To avoid ROS toxicity, plants are armed with different enzymatic and non-enzymatic systems to decompose ROS. Among the enzymatic system, CAT proteins are well studied. CAT not only controls growth and development in plants but is also involved in plant defense against different stresses. So far, the CAT gene family has not been reported in durum wheat (Triticum turgidum ssp. durum L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the durum wheat genome. Here, six TdCAT genes were identified. Based on phylogenetics, the TdCAT genes belong to three groups (Groups I–III) which is explainable by their comparable structural characteristics. Using bio-informatic analysis, we found that the secondary and tertiary structures were conserved among plants and present similar structures among durum wheat CATs. Two conserved domains (pfam00199 and pfam06628) are also present in all identified proteins, which have different subcellular localizations: peroxisome and mitochondrion. By analyzing their promoters, different cis-elements were identified, such as hormone-correlated response and stress-related responsive elements. Finally, we studied the expression pattern of two catalase genes belonging to two different sub-classes under different abiotic stresses. Expression profiling revealed that TdCAT2 and TdCAT3 presented a constitutive expression pattern. Moreover, both genes are induced in response to salt, mannitol, cold, heat and ABA. Thus, we speculate that those genes are activated by different stresses, such as oxygen deficiency, light, cold, abscisic acid and methyl jasmonate. Further, this study will help in understanding the behavior of CAT genes during environmental stress in durum wheat and in Triticeae species in general. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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11 pages, 2979 KiB  
Article
Metagenomic Sequencing to Analyze Composition and Function of Top-Gray Chalky Grain Microorganisms from Hybrid Rice Seeds
by You Liu, Yuan Yuan, Hui Yuan, Yan Wang, Chenzhong Jin, Hao Zhang, Jianliang Tang and Yihong Hu
Plants 2023, 12(12), 2358; https://doi.org/10.3390/plants12122358 - 18 Jun 2023
Viewed by 951
Abstract
The top-gray chalkiness of hybrid rice (Oryza sativa L.) seeds is a typical phenomenon in hybrid rice seeds. The chalky part of the grain is infected and is the inoculum to infect the normal seeds during storage and soaking. These seed-associated microorganisms [...] Read more.
The top-gray chalkiness of hybrid rice (Oryza sativa L.) seeds is a typical phenomenon in hybrid rice seeds. The chalky part of the grain is infected and is the inoculum to infect the normal seeds during storage and soaking. These seed-associated microorganisms were cultivated and sequenced using metagenomics shotgun sequencing to obtain more comprehensive information on the seed-associated microorganisms in this experiment. The results showed that fungi could grow well on the rice flour medium, similar to the ingredients of rice seed endosperms. After the assembly of metagenomic data, a gene catalog was established, comprising 250,918 genes. Function analysis showed that glycoside hydrolases were the dominant enzymes, and the genus Rhizopus accounted for the dominant microorganisms. The fungal species R. microspores, R. delemar, and R. oryzae were likely to be the candidate pathogens in the top-gray chalky grains of hybrid rice seeds. These results will provide a reference for improving hybrid rice processing after harvest. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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23 pages, 5910 KiB  
Article
Genome-Wide Identification and Expression Profiling of Pathogenesis-Related Protein 1 (PR-1) Genes in Durum Wheat (Triticum durum Desf.)
by Ikram Zribi, Mouna Ghorbel, Najla Haddaji, Malek Besbes and Faiçal Brini
Plants 2023, 12(10), 1998; https://doi.org/10.3390/plants12101998 - 16 May 2023
Cited by 5 | Viewed by 1638
Abstract
Pathogen-related proteins (PRs) are diversified proteins with a low molecular weight implicated in plant response to biotic and abiotic stress as well in regulating different functions in plant maturation. Interestingly, no systematical study has been conducted in durum wheat (Triticum turgidum subsp. [...] Read more.
Pathogen-related proteins (PRs) are diversified proteins with a low molecular weight implicated in plant response to biotic and abiotic stress as well in regulating different functions in plant maturation. Interestingly, no systematical study has been conducted in durum wheat (Triticum turgidum subsp. durum). In the present study, 12 PR-1 genes encoding a CAP superfamily domain were identified in the genome of Triticum turgidum subsp. durum, which is an important cereal, using in silico approaches. Additionally, phylogenetic analysis showed that the PR-1 genes were classified into three groups based on their isoelectric point and the conserved motif domain. Moreover, our analysis showed that most of the TdPR-1 proteins presented an N-terminal signal peptide. Expression patterns analysis showed that the PR-1 gene family presented temporal and spatial specificity and was induced by different abiotic stresses. This is the first report describing the genome-scale analysis of the durum wheat PR-1 gene family, and these data will help further study the roles of PR-1 genes during stress responses, leading to crop improvement. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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23 pages, 2795 KiB  
Article
LSPpred Suite: Tools for Leaderless Secretory Protein Prediction in Plants
by Andrew Lonsdale, Laura Ceballos-Laita, Daisuke Takahashi, Matsuo Uemura, Javier Abadía, Melissa J. Davis, Antony Bacic and Monika S. Doblin
Plants 2023, 12(7), 1428; https://doi.org/10.3390/plants12071428 - 23 Mar 2023
Viewed by 1596
Abstract
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of [...] Read more.
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of contamination from other subcellar compartments upon purification of the secretome. Applying machine learning algorithms to predict LSPs in plants is also challenging due to the rarity of experimentally validated examples for training purposes. This work attempts to address this issue by establishing criteria for identifying potential plant LSPs based on experimental observations and training random forest classifiers on the putative datasets. The resultant plant protein database LSPDB and bioinformatic prediction tools LSPpred and SPLpred are available at lsppred.lspdb.org. The LSPpred and SPLpred modules are internally validated on the training dataset, with false positives controlled at 5%, and are also able to classify the limited number of established plant LSPs (SPLpred (3/4, LSPpred 4/4). Until such time as a larger set of bona fide (independently experimentally validated) LSPs is established using imaging technologies (light/fluorescence/electron microscopy) to confirm sub-cellular location, these tools represent a bridging method for predicting and identifying plant putative LSPs for subsequent experimental validation. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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17 pages, 8664 KiB  
Article
OliveAtlas: A Gene Expression Atlas Tool for Olea europaea
by Amanda Bullones, Antonio Jesús Castro, Elena Lima-Cabello, Juan de Dios Alché, Francisco Luque, Manuel Gonzalo Claros and Noe Fernandez-Pozo
Plants 2023, 12(6), 1274; https://doi.org/10.3390/plants12061274 - 10 Mar 2023
Cited by 2 | Viewed by 2162
Abstract
The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding [...] Read more.
The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the ‘Picual’ genome reference and gene annotation. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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12 pages, 3293 KiB  
Article
MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica
by Aynhoa Gómez-Ollé, Amanda Bullones, Jose I. Hormaza, Lukas A. Mueller and Noe Fernandez-Pozo
Plants 2023, 12(6), 1273; https://doi.org/10.3390/plants12061273 - 10 Mar 2023
Cited by 3 | Viewed by 2196
Abstract
Mango (Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated [...] Read more.
Mango (Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated in more than 100 countries, with a production of more than 40 million tons. Recently the genome sequences of several mango varieties have been released, but there are no bioinformatics platforms dedicated to mango genomics and breeding to host mango omics data. Here, we present MangoBase, a web portal dedicated to mango genomics, which provides multiple interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. Additionally, MangoBase includes a gene expression atlas with 12 datasets and 80 experiments representing some of the most significant mango RNA-seq experiments published to this date. These experiments study mango fruit ripening in several cultivars with different pulp firmness and sweetness or peel coloration, and other experiments also study hot water postharvest treatment, infection with C. gloeosporioides, and the main mango tree organ tissues. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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17 pages, 4364 KiB  
Article
Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids
by Manfred Ritz, Nadim Ahmad, Thomas Brueck and Norbert Mehlmer
Plants 2023, 12(3), 632; https://doi.org/10.3390/plants12030632 - 01 Feb 2023
Cited by 5 | Viewed by 1704
Abstract
Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced [...] Read more.
Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced on a genomic level. Functional annotation of genes as well as comparative genome analysis on long read datasets enabled the identification of cultivar-specific terpene synthase and cytochrome p450 enzyme sequences. This enables new insights, especially since terpenoids in research and industry are gaining increasing interest due to their importance in areas such as food preservation, fragrances, or as active ingredients in pharmaceutical formulations. According to BUSCO assessments, the presented genomes have an average size of 355 Mb and about 96.8% completeness. An average of 52,090 genes could be annotated as putative proteins, whereas about 42 were associated with terpene synthases and about 1340 with cytochrome p450 enzymes. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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17 pages, 2634 KiB  
Article
Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight
by Martín Moret, Jorge A. Ramírez-Tejero, Alicia Serrano, Elena Ramírez-Yera, María D. Cueva-López, Angjelina Belaj, Lorenzo León, Raúl de la Rosa, Aureliano Bombarely and Francisco Luque
Plants 2023, 12(1), 155; https://doi.org/10.3390/plants12010155 - 29 Dec 2022
Cited by 6 | Viewed by 1964
Abstract
The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive [...] Read more.
The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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27 pages, 6802 KiB  
Article
Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of PLATZ Gene Family Members in Solanum Lycopersicum L. under Multiple Abiotic Stresses
by Antt Htet Wai, Md Mustafizur Rahman, Muhammad Waseem, Lae-Hyeon Cho, Aung Htay Naing, Jong-Seong Jeon, Do-jin Lee, Chang-Kil Kim and Mi-Young Chung
Plants 2022, 11(22), 3112; https://doi.org/10.3390/plants11223112 - 15 Nov 2022
Cited by 5 | Viewed by 1897
Abstract
PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, [...] Read more.
PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, but their role in tomato has not been explored yet. In the present work, 20 non-redundant Solanum lycopersicum PLATZ (SlPLATZ) genes with three segmentally duplicated gene pairs and four tandemly duplicated gene pairs were identified on eight tomato chromosomes. The comparative modeling and gene ontology (GO) annotations of tomato PLATZ proteins indicated their probable roles in defense response, transcriptional regulation, and protein metabolic processes as well as their binding affinity for various ligands, including nucleic acids, peptides, and zinc. SlPLATZ10 and SlPLATZ17 were only expressed in 1 cm fruits and flowers, respectively, indicating their preferential involvement in the development of these organs. The expression of SlPLATZ1, SlPLATZ12, and SlPLATZ19 was up- or down-regulated following exposure to various abiotic stresses, whereas that of SlPLATZ11 was induced under temperature stresses (i.e., cold and heat stress), revealing their probable function in the abiotic stress tolerance of tomato. Weighted gene co-expression network analysis corroborated the aforementioned findings by spotlighting the co-expression of several stress-associated genes with SlPLATZ genes. Confocal fluorescence microscopy revealed the localization of SlPLATZ–GFP fusion proteins in the nucleus, hinting at their functions as transcription factors. These findings provide a foundation for a better understanding of the structure and function of PLATZ genes and should assist in the selection of potential candidate genes involved in the development and abiotic stress adaptation in tomato. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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18 pages, 3947 KiB  
Article
Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species
by Qi Jin, Zitian Yang, Wenjing Yang, Xiaoyang Gao and Changning Liu
Plants 2022, 11(18), 2397; https://doi.org/10.3390/plants11182397 - 14 Sep 2022
Cited by 1 | Viewed by 1297
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study [...] Read more.
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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15 pages, 11145 KiB  
Article
Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss
by Morteza Sheikh-Assadi, Roohangiz Naderi, Seyed Alireza Salami, Mohsen Kafi, Reza Fatahi, Vahid Shariati, Federico Martinelli, Angela Cicatelli, Maria Triassi, Francesco Guarino, Giovanni Improta and Manuel Gonzalo Claros
Plants 2022, 11(18), 2365; https://doi.org/10.3390/plants11182365 - 10 Sep 2022
Cited by 2 | Viewed by 1880
Abstract
A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of [...] Read more.
A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed and compared using 11 constructed transcriptomes. Concisely, normalized benchmarking demonstrated that Velvet–Oases suffer from the worst results, while the EvidentialGene strategy can provide the most comprehensive and accurate transcriptome of Lilium ledebourii (Baker) Boiss. The BLAST results also confirmed the superiority of EvidentialGene, so it could capture even up to 59% more (than Velvet–Oases) unique gene hits. To promote assembly optimization, with the help of normalized benchmarking, PCA and AHC, it is emphasized that each metric can only provide part of the transcriptome status, and one should never settle for just a few evaluation criteria. This study supplies a framework for benchmarking and optimizing the efficiency of assembly approaches to analyze RNA-Seq data and reveals that selecting an inefficient assembly strategy might result in less identification of unique gene hits. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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27 pages, 4258 KiB  
Article
Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae
by Eugenia I. Bondar, Sergey I. Feranchuk, Ksenia A. Miroshnikova, Vadim V. Sharov, Dmitry A. Kuzmin, Natalya V. Oreshkova and Konstantin V. Krutovsky
Plants 2022, 11(15), 2062; https://doi.org/10.3390/plants11152062 - 06 Aug 2022
Cited by 8 | Viewed by 2617
Abstract
The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in [...] Read more.
The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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13 pages, 2277 KiB  
Article
Genome-Wide Characterization and Expression Analysis of GeBP Family Genes in Soybean
by Sushuang Liu, Yanmin Liu, Chundong Liu, Feixue Zhang, Jiaping Wei and Bingxuan Li
Plants 2022, 11(14), 1848; https://doi.org/10.3390/plants11141848 - 14 Jul 2022
Cited by 5 | Viewed by 1546
Abstract
The glabrous-enhancer-binding protein (GeBP) family is a family of plant-specific transcription factors, whose members share a central DNA-binding domain. Previous studies have already proven that GeBP genes are involved in the control of cell expansion but not cell proliferation in Arabidopsis. However, [...] Read more.
The glabrous-enhancer-binding protein (GeBP) family is a family of plant-specific transcription factors, whose members share a central DNA-binding domain. Previous studies have already proven that GeBP genes are involved in the control of cell expansion but not cell proliferation in Arabidopsis. However, there has not yet been a versatile analysis of the GeBP genes’ function in soybean (Glycine max L.). Here, we identified and named 9 GmGeBP genes in the soybean genome. These genes were distributed on 7 of the 20 chromosomes and the intron numbers ranged from zero to one. According to the phylogenetic tree, 52 GeBP genes obtained from four plant species were clustered into major four groups. Through the RNA-seq analysis of the nine GmGeBP genes, 8 of 9 GmGeBP genes were be found to expressed differentially across the 14 tissues. Additionally, among nine GmGeBP genes, only GeBP4 were highly expressed in abnormal trichome soybeans, which was predicted to be involved in trichome development. This genome-wide analysis of GmGeBP genes helps to provide an overview of the evolution and functions of two kinds of soybean plants. These results will help to clarify the potential functions and characteristics of GmGeBP genes in the soybean life cycle. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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Review

Jump to: Research

24 pages, 1583 KiB  
Review
Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom
by Muhammad-Redha Abdullah-Zawawi, Nisha Govender, Sarahani Harun, Nor Azlan Nor Muhammad, Zamri Zainal and Zeti-Azura Mohamed-Hussein
Plants 2022, 11(19), 2614; https://doi.org/10.3390/plants11192614 - 05 Oct 2022
Cited by 3 | Viewed by 2786
Abstract
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source [...] Read more.
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Resources and Omics)
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