scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

2020 ◽  
Author(s):  
Yuxin Pan ◽  
Jinpeng Wang ◽  
Zhenyi Wang ◽  
Hengwei Liu ◽  
Lan Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Cotton Species ◽  
Expressional Analysis ◽  
Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

scholarly journals Genome-wide analysis and expression characteristics of small auxin-up RNA (SAUR) genes in moso bamboo (Phyllostachys edulis)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 325-336 ◽  
Author(s):  
Qingsong Bai ◽  
Dan Hou ◽  
Long Li ◽  
Zhanchao Cheng ◽  
Wei Ge ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Shoot Growth ◽  
Subcellular Location ◽  
Moso Bamboo ◽  
Pcr Analysis ◽  
Phyllostachys Edulis ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Gene Structures

Moso bamboo (Phyllostachys edulis) is well known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny, and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and that the PheSAUR genes were differentially expressed. Furthermore, quantitative real-time PCR analysis indicated that all of the PheSAUR genes could be induced in different tissues of seedlings and that 37 (except PheSAUR41) of the PheSAUR genes were up-regulated after indole-3-acetic acid (IAA) treatment. These results reveal a comprehensive overview of the PheSAUR gene family and may pave the way for deciphering their functions during bamboo development.

scholarly journals Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration

2020 ◽  
Vol 21 (6) ◽  
pp. 2188
Author(s):  
Miaomiao Qin ◽  
Jing Wang ◽  
Tianyi Zhang ◽  
Xiangyang Hu ◽  
Rui Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Control Group ◽  
Binding Motif ◽  
Isatis Indigotica ◽  
Rate Limiting Step ◽  
Genome Wide ◽  
Transgenic Lines ◽  
Gene Structures ◽  
High Auxin

Auxin is one of the most critical hormones in plants. YUCCA (Tryptophan aminotransferase of Arabidopsis (TAA)/YUCCA) enzymes catalyze the key rate-limiting step of the tryptophan-dependent auxin biosynthesis pathway, from IPA (Indole-3-pyruvateacid) to IAA (Indole-3-acetic acid). Here, 13 YUCCA family genes were identified from Isatis indigotica, which were divided into four categories, distributing randomly on chromosomes (2n = 14). The typical and conservative motifs, including the flavin adenine dinucleotide (FAD)-binding motif and flavin-containing monooxygenases (FMO)-identifying sequence, existed in the gene structures. IiYUCCA genes were expressed differently in different organs (roots, stems, leaves, buds, flowers, and siliques) and developmental periods (7, 21, 60, and 150 days after germination). Taking IiYUCCA6-1 as an example, the YUCCA genes functions were discussed. The results showed that IiYUCCA6-1 was sensitive to PEG (polyethylene glycol), cold, wounding, and NaCl treatments. The over-expressed tobacco plants exhibited high auxin performances, and some early auxin response genes (NbIAA8, NbIAA16, NbGH3.1, and NbGH3.6) were upregulated with increased IAA content. In the dark, the contents of total chlorophyll and hydrogen peroxide in the transgenic lines were significantly lower than in the control group, with NbSAG12 downregulated and some delayed leaf senescence characteristics, which delayed the senescence process to a certain extent. The findings provide comprehensive insight into the phylogenetic relationships, chromosomal distributions, and expression patterns and functions of the YUCCA gene family in I. indigotica.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengyuan Wei ◽  
Aili Liu ◽  
Yujuan Zhang ◽  
Yong Zhou ◽  
Donghua Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Genome Wide ◽  
Gene Structures ◽  
Relationship Of ◽  
Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

scholarly journals Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ting Zhu ◽  
Yue Liu ◽  
Liting Ma ◽  
Xiaoying Wang ◽  
Dazhong Zhang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Gene Structure ◽  
Expression Patterns ◽  
Wheat Yield ◽  
Chromosomal Distribution ◽  
Positive Role ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events

Abstract Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

scholarly journals Genome-Wide Identification of the NHX Gene Family in Punica granatum L. and Their Expressional Patterns under Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 264
Author(s):  
Jianmei Dong ◽  
Cuiyu Liu ◽  
Yuying Wang ◽  
Yujie Zhao ◽  
Dapeng Ge ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Tertiary Structure ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Punica Granatum ◽  
Conserved Motifs ◽  
Cis Acting ◽  
Gene Structures ◽  
Punica Granatum L

Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl− and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate.

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