scholarly journals Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Qi Yang ◽  
Xiaocui Niu ◽  
Xiaona Tian ◽  
Xiujuan Zhang ◽  
Jingyu Cong ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Genomic Analysis ◽  
Gene Families ◽  
Land Plant ◽  
Biological Functions ◽  
Phylogenetic Groups ◽  
Functional Conservation ◽  
Group I

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.

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 ◽  
...  
Keyword(s):  
Gene Family ◽  
Phospholipase C ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Genomic Analysis

scholarly journals Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants

2016 ◽  
Vol 8 (3) ◽  
pp. 791-810 ◽  
Author(s):  
Yan-Li Chang ◽  
Wen-Yan Li ◽  
Hai Miao ◽  
Shuai-Qi Yang ◽  
Ri Li ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Abiotic Stresses ◽  
Genomic Analysis ◽  
Gene Families

scholarly journals Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jie Xiao ◽  
Rui Hu ◽  
Ting Gu ◽  
Jiapeng Han ◽  
Ding Qiu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Genome Wide

Comprehensive genomic analysis and expression profiling of diacylglycerol kinase gene family in Malus prunifolia (Willd.) Borkh

Gene ◽  
2015 ◽  
Vol 561 (2) ◽  
pp. 225-234 ◽  
Author(s):  
Yali Li ◽  
Yanxiao Tan ◽  
Yun Shao ◽  
Mingjun Li ◽  
Fengwang Ma
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Genomic Analysis ◽  
Diacylglycerol Kinase ◽  
Kinase Gene ◽  
Malus Prunifolia

Genome-Wide Identification and Expression Profiling of the ERF Gene Family in Medicago sativa L. Under Various Abiotic Stresses

2019 ◽  
Vol 38 (10) ◽  
pp. 1056-1068 ◽  
Author(s):  
Xiaoyu Jin ◽  
Xiaofan Yin ◽  
Boniface Ndayambaza ◽  
Zhengshe Zhang ◽  
Xueyang Min ◽  
...  
Keyword(s):  
Gene Family ◽  
Medicago Sativa ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Genome Wide ◽  
Medicago Sativa L

scholarly journals Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8467 ◽  
Author(s):  
Lin Zhang ◽  
Wei Chen ◽  
Ben Shi
Keyword(s):  
Transcription Factor ◽  
Heat Shock ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Gene Families ◽  
Heat Shock Transcription Factor ◽  
Physic Nut ◽  
Genome Wide ◽  
Transcription Factor Gene Family

The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.

scholarly journals Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

2021 ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers

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.

scholarly journals Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Luzhao Pan ◽  
Jiaqiu Zheng ◽  
Jia Liu ◽  
Jun Guo ◽  
Fawan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Pepper Plant ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Group I

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

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