scholarly journals Comprehensive Genomic Analysis and Expression Profiling of Phospholipase C Gene Family during Abiotic Stresses and Development in Rice

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62494 ◽  
Author(s):  
Amarjeet Singh ◽  
Poonam Kanwar ◽  
Amita Pandey ◽  
Akhilesh K. Tyagi ◽  
Sudhir K. Sopory ◽  
...  
BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Qi Yang ◽  
Xiaocui Niu ◽  
Xiaona Tian ◽  
Xiujuan Zhang ◽  
Jingyu Cong ◽  
...  

Abstract Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.


BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jie Xiao ◽  
Rui Hu ◽  
Ting Gu ◽  
Jiapeng Han ◽  
Ding Qiu ◽  
...  

Gene ◽  
2015 ◽  
Vol 561 (2) ◽  
pp. 225-234 ◽  
Author(s):  
Yali Li ◽  
Yanxiao Tan ◽  
Yun Shao ◽  
Mingjun Li ◽  
Fengwang Ma

2019 ◽  
Vol 38 (10) ◽  
pp. 1056-1068 ◽  
Author(s):  
Xiaoyu Jin ◽  
Xiaofan Yin ◽  
Boniface Ndayambaza ◽  
Zhengshe Zhang ◽  
Xueyang Min ◽  
...  

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0138467 ◽  
Author(s):  
Fawei Wang ◽  
Yu Deng ◽  
Yonggang Zhou ◽  
Jinye Dong ◽  
Huan Chen ◽  
...  

2021 ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming

Abstract DNA-binding with one finger (Dof) transcription factors are plant-specific transcription factors involved in numerous pathways of plant development, especially in respond to abiotic stresses. Although genome-wide analysis of this gene family has been performed in many species, Dof genes in spinach have not been thoroughly analyzed. We performed a genome-wide analysis and characterization of Dof gene family in spinach. Twenty two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purify selection. Using Cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.


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