scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

scholarly journals Genome-wide investigation of Hydroxycinnamoyl CoA: Shikimate Hydroxycinnamoyl Transferase (HCT) gene family in Carthamus tinctorius L.

2021 ◽  
Vol 49 (3) ◽  
pp. 12489
Author(s):  
Sun FAN ◽  
Naveed AHMAD ◽  
Jin LIBO ◽  
Zhang XINYUE ◽  
Ma XINTONG ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Carthamus Tinctorius ◽  
Plant Growth And Development ◽  
Monolignol Biosynthesis ◽  
Genome Wide ◽  
Wide Range

Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) is mainly associated with monolignol biosynthesis, a central precursor to producing guaiacyl and syringyl lignins in plants. However, the explicit regulatory mechanism of HCT-mediated monolignol biosynthesis in plants still remained unclear. Here, the genome-wide analysis of the HCT gene family in Carthamus tinctorius as a target for understanding growth, development, and stress-responsive mechanisms was investigated. A total of 82 CtHCT genes were identified and characterized. Most of the CtHCTs proteins demonstrated the presence of two common conserved domains, including HXXXD and DFGWG. In addition, the conserved structure of protein motifs, PPI network, cis-regulatory units, and gene structure analysis demonstrated several genetic determinants reflecting the wide range of functional diversity of CtHCT-encoding genes. The observed expression analysis of CtHCT genes in different flowering stages under normal conditions partially highlighted their putative roles in plant growth and development pathways. Moreover, CtHCT genes appeared to be associated with abiotic stress responses as validated by the expression profiling in various flowering phases under light irradiation and MeJA treatment. Altogether, these findings provide new insights into identifying crucial molecular targets associated with plant growth and development and present practical information for understanding abiotic stress-responsive mechanisms in plants.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 972
Author(s):  
Won-Hee Kang ◽  
Boseul Park ◽  
Junesung Lee ◽  
Seon-In Yeom
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Capsicum Annuum ◽  
Growth And Development ◽  
Function Analysis ◽  
Dry Weight ◽  
Defense Responses ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Biotic Stresses

Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in response to multiple biotic stresses. To further understand the role of CaRLPs in plant growth and development, we analyzed expression patterns of all CaRLPs from various pepper tissues and developmental stages using RNA-seq. Ten CaRLP genes were selected for further analysis according to transcript levels with hierarchical clustering. The selected CaRLP genes displayed similarity of motifs within the same groups and structures typical of RLPs. To examine RLP function in growth and development, we performed loss-of-function analysis using a virus-induced gene silencing system. Three of the ten tested CaRLPs (CaRLP238, 253, and 360) in silenced plants exhibited phenotypic alteration with growth retardation compared to controls. All three gene-silenced peppers showed significant differences in root dry weight. Only CaRLP238 had significant differences in both root and shoot dry weight. Our results suggest that CaRLPs may play important roles in regulation of plant growth and development as well as function in defense responses to biotic stresses in the RLP gene family.

scholarly journals Functions of PPR Proteins in Plant Growth and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11274
Author(s):  
Xiulan Li ◽  
Mengdi Sun ◽  
Shijuan Liu ◽  
Qian Teng ◽  
Shihui Li ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Responses ◽  
Rna Processing ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Plant Mitochondria ◽  
Research Progress ◽  
Plant Growth And Development ◽  
Ppr Proteins

Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.

scholarly journals Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9551
Author(s):  
Lidong Hao ◽  
Shubing Shi ◽  
Haibin Guo ◽  
Ming Li ◽  
Pan Hu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Growth And Development ◽  
Expression Profiles ◽  
Vital Role ◽  
Ethylene Response Factor ◽  
Plant Growth And Development ◽  
Element Analysis ◽  
Genome Wide ◽  
Genes Expression

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

scholarly journals Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

2020 ◽  
Vol 21 (3) ◽  
pp. 975 ◽  
Author(s):  
Xiaojun Pu ◽  
Lixin Yang ◽  
Lina Liu ◽  
Xiumei Dong ◽  
Silin Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Physcomitrella Patens ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Terrestrial Environments ◽  
Gene Structures ◽  
Myb Genes ◽  
Myb Proteins ◽  
R2r3 Myb

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

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, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

2016 ◽  
Vol 17 (7) ◽  
pp. 1004 ◽  
Author(s):  
Wei Xu ◽  
Zexi Chen ◽  
Naeem Ahmed ◽  
Bing Han ◽  
Qinghua Cui ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Gras Gene
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