scholarly journals Phylogeny and Functions of LOB Domain Proteins in Plants

2020 ◽  
Vol 21 (7) ◽  
pp. 2278 ◽  
Author(s):  
Yuwen Zhang ◽  
Ziwen Li ◽  
Biao Ma ◽  
Quancan Hou ◽  
Xiangyuan Wan
Keyword(s):  
Functional Diversity ◽  
Family Members ◽  
Biological Significance ◽  
Gene Families ◽  
Plant Growth And Development ◽  
Functional Characteristics ◽  
Functional Studies ◽  
Genome Wide ◽  
Lateral Organ ◽  
Phylogenetic Framework

Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.

scholarly journals Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum

2019 ◽  
Vol 20 (21) ◽  
pp. 5360 ◽  
Author(s):  
Hengzhi Liu ◽  
Minxuan Cao ◽  
Xiaoli Chen ◽  
Minghui Ye ◽  
Peng Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Plant Growth And Development ◽  
Point Distribution ◽  
Expression Levels ◽  
Genome Wide Analysis ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Normal Metabolism ◽  
Lateral Organ ◽  
Organ Boundaries

Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes’ resistance to drought.

scholarly journals Genome-wide identification and expression profiling of invertase gene family for abiotic stresses tolerance in Poncirus trifoliata

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bachar Dahro ◽  
Yue Wang ◽  
Ahmed Alhag ◽  
Chunlong Li ◽  
Dayong Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Family Members ◽  
Physiological Role ◽  
Poncirus Trifoliata ◽  
High Accumulation ◽  
Functional Studies ◽  
Genome Wide ◽  
Cold Tolerant

Abstract Background Sucrose (Suc) hydrolysis is directly associated with plants tolerance to multiple abiotic stresses. Invertase (INV) enzymes irreversibly catalyze Suc degradation to produce glucose (Glc) and fructose (Frc). However, genome-wide identification and function of individual members of the INV gene family in Poncirus trifoliata or its Citrus relatives in response to abiotic stresses are not fully understood. Results In this report, fourteen non-redundant PtrINV family members were identified in P. trifoliata including seven alkaline/neutral INV genes (PtrA/NINV1–7), two vacuolar INV genes (PtrVINV1–2), and five cell wall INV isoforms (PtrCWINV1–5). A comprehensive analysis based on the biochemical characteristics, the chromosomal location, the exon–intron structures and the evolutionary relationships demonstrated the conservation and the divergence of PtrINVs. In addition, expression analysis of INV genes during several abiotic stresses in various tissues indicated the central role of A/NINV7 among INV family members in response to abiotic stresses. Furthermore, our data demonstrated that high accumulation of Suc, Glc, Frc and total sugar contents were directly correlated with the elevated activities of soluble INV enzymes in the cold-tolerant P. trifoliata, C. ichangensis and C. sinensis, demonstrating the potential role of soluble INV enzymes for the cold tolerance of Citrus. Conclusions This work offered a framework for understanding the physiological role of INV genes and laid a foundation for future functional studies of these genes in response to abiotic stresses.

scholarly journals Genome-wide characterization and expression analysis of PP2CA family members in response to ABA and osmotic stress in Gossypium

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7105 ◽  
Author(s):  
Tingting Lu ◽  
Gaofeng Zhang ◽  
Yibin Wang ◽  
Shibin He ◽  
Lirong Sun ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Expression Patterns ◽  
Family Members ◽  
Purifying Selection ◽  
Gene Families ◽  
Negative Control ◽  
Genome Wide ◽  
Control Growth ◽  
Cotton Species ◽  
Aba Receptors

Clade A type 2C protein phosphatases (PP2CAs), as central regulators of abscisic acid (ABA) signaling, negative control growth, development and responses to multiple stresses in plants. PP2CA gene families have been characterized at genome-wide levels in several diploid plants like Arabidopsis and rice. However, the information about genome organization, phylogenesis and putative functions of PP2CAs in Gossypium is lacking. Here, PP2CA family members were comprehensively analyzed in four Gossypium species including the diploid progenitor Gossypium arboreum, G. raimondii and the tetraploid G. hirsutum and G. barbadense, and 14, 13, 27, and 23 PP2CA genes were identified in the genomic sequences of these plants, respectively. Analysis results showed that most Gossypium PP2CAs were highly conserved in chromosomal locations, structures, and phylogeny among the four cotton species. Segmental duplication might play important roles in the formation of the PP2CAs, and most PP2CAs may be under purifying selection in Gossypium during evolution. The majority of the PP2CAs were expressed specifically in diverse tissues, and highly expressed in flowers in G. hirsutum. The GhPP2CAs displayed diverse expression patterns in responding to ABA and osmotic stress. Yeast-two hybrid assays revealed that many GhPP2CAs were capable of interaction with the cotton ABA receptors pyrabactin resistance1/PYR1-like/regulatory components of ABA receptors (PYR1/PYL/RCAR) GhPYL2-2D (Gh_D08G2587), GhPYL6-2A (Gh_A06G1418), and GhPYL9-2A (Gh_A11G0870) in the presence and/or absence of ABA. These results gave a comprehensive view of the Gossypium PP2CAs and are valuable for further studying the functions of PP2CAs in Gossypium.

scholarly journals Composite plants for a composite plant: An efficient protocol for root studies in the sunflower using composite plants approach

2019 ◽  
Author(s):  
Tyler Parks ◽  
Yordan S. Yordanov
Keyword(s):  
Gene Families ◽  
Oilseed Crop ◽  
Transgenic Roots ◽  
Gene Characterization ◽  
Composite Plants ◽  
Functional Studies ◽  
Rate Limiting Step ◽  
Genome Wide ◽  
Related Transcription Factor ◽  
Sunflower Genome

AbstractSunflower (Helianthus annuus L.) is important oilseed crop in the world and the sunflower oil is prized for its’ exceptional quality and flavor. The recent availability of the sunflower genome can allow genome-wide characterization of genes and gene families. With plant transformation usually being the rate limiting step for gene functional studies of sunflower, composite plants can alleviate this bottleneck. Composite plants, produced using Agrobacterium rhizogenes, are plants with transgenic roots and wild type shoots. Composite plants offer benefits over creating fully transgenic plants, namely time and cost. Here we outlined the critical steps and parameters for a protocol for the sunflower composite plants production. We use more than a dozen genotypes and three constitutive promoters to validates the utility and efficiency of this protocol. Moreover, functional gene characterization by overexpression and RNAi silencing of a root related transcription factor HaLBD16 further emphasize the value of the system in the sunflower studies. With the protocol developed here an experiment can be carried out with efficiency and in only two months. This procedure adds to arsenal of approaches for the functional genetics/genomics in sunflower for characterization candidate genes involved in root development and stress adaptation.Key messageComposite plants technique described here is fast and efficient approach for roots functional studies in sunflower.

scholarly journals Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shuquan Rao ◽  
Yao Yao ◽  
Daniel E. Bauer
Keyword(s):  
Genome Editing ◽  
Genetic Variants ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Functional Studies ◽  
Functional Genetics ◽  
Genome Wide ◽  
Causal Variants ◽  
Experimental Approaches

AbstractGenome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly noncoding, have an impact on associated diseases and traits remains a significant hurdle. In this review, we discuss emerging experimental approaches that are being applied for functional studies of causal variants and translational advances from GWAS findings to disease prevention and treatment. We highlight the use of genome editing technologies in GWAS functional studies to modify genomic sequences, with proof-of-principle examples. We discuss the challenges in interrogating causal variants, points for consideration in experimental design and interpretation of GWAS locus mechanisms, and the potential for novel therapeutic opportunities. With the accumulation of knowledge of functional genetics, therapeutic genome editing based on GWAS discoveries will become increasingly feasible.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

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