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

scholarly journals Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

2018 ◽  
Author(s):  
Guodong Chen ◽  
Xiaolong Li ◽  
Xin qiao ◽  
Jiaming Li ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Higher Plants ◽  
Chloride Transport ◽  
Structural Characteristics ◽  
Evolutionary Analysis ◽  
Anion Channels ◽  
Genome Wide ◽  
A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

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 identification and comparative analysis of Dof gene family in Brassica napus

2020 ◽  
Author(s):  
Neeta Lohani ◽  
Saeid Babaei ◽  
Mohan B. Singh ◽  
Prem L. Bhalla
Keyword(s):  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Stress Responses ◽  
Structure Evolution ◽  
Oilseed Crop ◽  
Evolutionary Analysis ◽  
Abiotic Stress Response ◽  
Protein Motifs ◽  
Genome Wide

AbstractDOF, DNA binding with one finger proteins are plant-specific transcription factors shown to play roles in diverse plant functions. However, a—little is known about DOF protein repertoire of the allopolyploid crop, Brassica napus. Here, we report genome-wide identification and systematic analysis of the Dof transcription factor family in this important oilseed crop. We identified 117 Brassica napus Dof genes (BnaDofs). So far, this is the largest number of Dof genes reported in a single eudicot species. Based on phylogenetic analysis, BnaDofs were classified into nine groups (A, B1, B2. C1, C2.1, C2.2, C3, D1, D2). Most members belonging to a particular group displayed conserved gene structural organisation and similar protein motifs distribution. Chromosomal localisation analysis highlighted the uneven distribution of BnaDofs across all chromosomes. Evolutionary analysis exemplified that the divergence of Brassica genus from Arabidopsis, the whole genome triplication event, and the hybridisation of B. oleracea and B. rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of Dof TF gene family in B. napus. Functional annotation of BnaDof proteins, cis-element analysis of their promoters suggested potential roles in organ development, the transition from vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness as well as abiotic stress responses. Furthermore, the transcriptomic analysis highlighted the preferential tissue-specific expression patters of BnaDofs and their role in response to various abiotic stress. Overall, this study provides a comprehensive understanding of the molecular structure, evolution, and potential functional roles of Dof genes in plant development and abiotic stress response.

scholarly journals Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10811
Author(s):  
Yanfeng Liu ◽  
Wei Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Epigenetic Modification ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
High Rate ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
And Function ◽  
Gras Gene

GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.

scholarly journals Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9225
Author(s):  
Yaoyao Jiang ◽  
Haichao Hu ◽  
Yuhua Ma ◽  
Junliang Zhou
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Evolutionary Analysis ◽  
Biotic And Abiotic Stress ◽  
Bioinformatic Tools ◽  
Genome Wide ◽  
Specific Analysis

Background The fibrillin (FBN) gene family is highly conserved and widely distributed in the photosynthetic organs of plants. Members of this gene family are involved in the growth and development of plants and their response to biotic and abiotic stresses. Wheat (Triticum aestivum), an important food crop, has a complex genetic background and little progress has occurred in the understanding of its molecular mechanisms. Methods In this study, we identified 26 FBN genes in the whole genome of T. aestivum through bioinformatic tools and biotechnological means. These genes were divided into 11 subgroups and were distributed on 11 chromosomes of T. aestivum. Interestingly, most of the TaFBN genes were located on the chromosomes 2A, 2B and 2D. The gene structure of each subgroup of gene family members and the position and number of motifs were highly similar. Results The evolutionary analysis results indicated that the affinities of FBNs in monocots were closer together. The tissue-specific analysis revealed that TaFBN genes were expressed in different tissues and developmental stages. In addition, some TaFBNs were involved in one or more biotic and abiotic stress responses. These results provide a basis for further study of the biological function of FBNs.

scholarly journals Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Nasreen Bano ◽  
Shafquat Fakhrah ◽  
Chandra Sekhar Mohanty ◽  
Sumit Kumar Bag
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Family Members ◽  
Regulatory Elements ◽  
Future Research ◽  
Tetraploid Cotton ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Salt And Drought Stress

Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.

scholarly journals Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

2021 ◽  
Author(s):  
Yongxian Tian ◽  
Qigang Wang ◽  
Hao Zhang ◽  
Ningning Zhou ◽  
Huijun Yan ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Mlo Gene Family
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