Genome-wide analysis of the barley MAPK gene family and its expression patterns in relation to Puccinia hordei infection

2015 ◽  
Vol 37 (11) ◽  
Author(s):  
Pavel Křenek ◽  
Rients E. Niks ◽  
Anton Vels ◽  
Petra Vyplelová ◽  
Jozef Šamaj
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Puccinia Hordei ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Mapk Gene

scholarly journals Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

2018 ◽  
Vol 19 (9) ◽  
pp. 2478 ◽  
Author(s):  
Qinglong Dong ◽  
Dingyue Duan ◽  
Shuang Zhao ◽  
Bingyao Xu ◽  
Jiawei Luo ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Sequence Alignments ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

scholarly journals Genome-Wide Analysis of MYB Gene Family in Chinese Bayberry (Morella rubra) and Identification of Members Regulating Flavonoid Biosynthesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yunlin Cao ◽  
Huimin Jia ◽  
Mengyun Xing ◽  
Rong Jin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Gene Family ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Structure Evolution ◽  
Chinese Bayberry ◽  
Genome Wide Analysis ◽  
Myb Gene ◽  
Genome Wide ◽  
Family Analysis

Chinese bayberry (Morella rubra), the most economically important fruit tree in the Myricaceae family, is a rich source of natural flavonoids. Recently the Chinese bayberry genome has been sequenced, and this provides an opportunity to investigate the organization and evolutionary characteristics of MrMYB genes from a whole genome view. In the present study, we performed the genome-wide analysis of MYB genes in Chinese bayberry and identified 174 MrMYB transcription factors (TFs), including 122 R2R3-MYBs, 43 1R-MYBs, two 3R-MYBs, one 4R-MYB, and six atypical MYBs. Collinearity analysis indicated that both syntenic and tandem duplications contributed to expansion of the MrMYB gene family. Analysis of transcript levels revealed the distinct expression patterns of different MrMYB genes, and those which may play important roles in leaf and flower development. Through phylogenetic analysis and correlation analyses, nine MrMYB TFs were selected as candidates regulating flavonoid biosynthesis. By using dual-luciferase assays, MrMYB12 was shown to trans-activate the MrFLS1 promoter, and MrMYB39 and MrMYB58a trans-activated the MrLAR1 promoter. In addition, overexpression of 35S:MrMYB12 caused a significant increase in flavonol contents and induced the expression of NtCHS, NtF3H, and NtFLS in transgenic tobacco leaves and flowers and significantly reduced anthocyanin accumulation, resulting in pale-pink or pure white flowers. This indicates that MrMYB12 redirected the flux away from anthocyanin biosynthesis resulting in higher flavonol content. The present study provides valuable information for understanding the classification, gene and motif structure, evolution and predicted functions of the MrMYB gene family and identifies MYBs regulating different aspects of flavonoid biosynthesis in Chinese bayberry.

scholarly journals Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Liu Zeng ◽  
Ang Gao ◽  
Yan Lv ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stress Conditions ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide ◽  
A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

scholarly journals Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl.

2021 ◽  
Vol 22 (19) ◽  
pp. 10269
Author(s):  
Li Zhang ◽  
Cheng Li ◽  
Danni Yang ◽  
Yuhua Wang ◽  
Yongping Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Class Ii ◽  
Class I ◽  
Genome Wide Analysis ◽  
Cell Proliferation And Differentiation ◽  
Genome Wide ◽  
A Genome ◽  
Transcription Factor Genes ◽  
Transient Activity

Teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family members are plant-specific transcription factors that regulate plant growth and development by controlling cell proliferation and differentiation. However, there are no reported studies on the TCP gene family in Dendrobium catenatum Lindl. Here, a genome-wide analysis of TCP genes was performed in D. catenatum, and 25 TCP genes were identified. A phylogenetic analysis classified the family into two clades: Class I and Class II. Genes in the same clade share similar conserved motifs. The GFP signals of the DcaTCP-GFPs were detected in the nuclei of tobacco leaf epidermal cells. The activity of DcaTCP4, which contains the miR319a-binding sequence, was reduced when combined with miR319a. A transient activity assay revealed antagonistic functions of Class I and Class II of the TCP proteins in controlling leaf development through the jasmonate-signaling pathway. After different phytohormone treatments, the DcaTCP genes showed varied expression patterns. In particular, DcaTCP4 and DcaTCP9 showed opposite trends after 3 h treatment with jasmonate. This comprehensive analysis provides a foundation for further studies on the roles of TCP genes in D. catenatum.

scholarly journals Genome-wide analysis of the Populus Hsp90 gene family reveals differential expression patterns, localization, and heat stress responses

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 532 ◽  
Author(s):  
Jin Zhang ◽  
Jianbo Li ◽  
Bobin Liu ◽  
Li Zhang ◽  
Jun Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Family ◽  
Differential Expression ◽  
Stress Responses ◽  
Expression Patterns ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-wide Analysis and Expression Profiling of SPS Gene Family in Brassica nupus L.

2018 ◽  
Vol 44 (2) ◽  
pp. 197
Author(s):  
Li ZHANG ◽  
Hong-Ju JIAN ◽  
Bo YANG ◽  
Ao-Xiang ZHANG ◽  
Chao ZHANG ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu
Keyword(s):  
Gene Family ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Type I ◽  
Black Raspberry ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genome Wide ◽  
Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

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