scholarly journals Identification and characterization of the Pvul-GASA gene family in the Phaseolus vulgaris and expression patterns under salt stress

2021 ◽  
Keyword(s):  
Salt Stress ◽  
Phaseolus Vulgaris ◽  
Gene Family ◽  
Expression Patterns ◽  
Identification And Characterization

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals Genome-wide identification and characterization of NF-Y gene family in peanut (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gene Duplication ◽  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Salt Stress Response

Abstract Background Nuclear factor Y (NF-Y) gene family consists of NF-YA, NF-YB and NF-YC subfamilies. Many members of NF-Y family have been involved in plant development processes, phytohormone signaling and tolerance to stresses in Arabidopsis and other plant species. However, little attention has been given in peanut. Results A total of 33 AhNF-Y genes (AhNF-Ys) were identified and distributed on 16 chromosomes. A phylogenetic analysis indicated that NF-Y genes prossessed highly conservatism in different plants. Gene duplication analyze indicated that only segmental duplication were detected. The abiotic stress-related regulatory elements analysis showed that AhNF-Ys, except for AhNF-YB6, contained at least one abiotic stress response element. With RNA-seq data, the tissue/organ-specific expression and differential expression profiling under salt stress were analyzed, indicating that six selected AhNF-Y gene may play potential roles in the regulation of salt stress response. qRT-PCR results suggested that these AhNF-Y genes also responded to osmotic, ABA (Abscisic Acid) and SA (Salicylic acid) stresses. Conclusions In this study, thirty three AhNF-Y genes were identified in cultivated peanut and the phylogeny, gene structures, motif composition, chromosomal location, gene duplication, stress-related regulatory elements, and expression patterns were also examined. These results may contribute to functional characterization of AhNF-Y genes in further research.

scholarly journals Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus

2019 ◽  
Vol 20 (22) ◽  
pp. 5749 ◽  
Author(s):  
Zhao ◽  
Liu ◽  
Zhang ◽  
Hu ◽  
Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Calvin Cycle ◽  
Regulatory Elements ◽  
Metabolic Enzyme ◽  
Genome Wide ◽  
Identification And Characterization

Fructose-1,6-bisphosphate aldolase (FBA) is a versatile metabolic enzyme involved in multiple important processes of glycolysis, gluconeogenesis, and Calvin cycle. Despite its significance in plant biology, the identity of this gene family in oil crops is lacking. Here, we performed genome-wide identification and characterization of FBAs in an allotetraploid species, oilseed rape Brassica napus. Twenty-two BnaFBA genes were identified and divided into two groups based on integrative analyses of functional domains, phylogenetic relationships, and gene structures. Twelve and ten B. napus FBAs (BnaFBAs) were predicted to be localized in the chloroplast and cytoplasm, respectively. Notably, synteny analysis revealed that Brassica-specific triplication contributed to the expansion of the BnaFBA gene family during the evolution of B. napus. Various cis-acting regulatory elements pertinent to abiotic and biotic stresses, as well as phytohormone responses, were detected. Intriguingly, each of the BnaFBA genes exhibited distinct sequence polymorphisms. Among them, six contained signatures of selection, likely having experienced breeding selection during adaptation and domestication. Importantly, BnaFBAs showed diverse expression patterns at different developmental stages and were preferentially highly expressed in photosynthetic tissues. Our data thus provided the foundation for further elucidating the functional roles of individual BnaFBA and also potential targets for engineering to improve photosynthetic productivity in B. napus.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

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