scholarly journals Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 16
Author(s):  
Yanjie Qu ◽  
Yaping Wang ◽  
Jun Zhu ◽  
Yugang Zhang ◽  
Hongmin Hou
Keyword(s):  
Abiotic Stress ◽  
Malus Domestica ◽  
Growth And Development ◽  
Expression Patterns ◽  
Specific Response ◽  
Nuclear Factor ◽  
Element Analysis ◽  
Nuclear Factor Y ◽  
Gene Structures ◽  
Y Family

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

scholarly journals NF-YB-Mediated Active Responses of Plant Growth under Salt and Temperature Stress in Eucalyptus grandis

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1107
Author(s):  
Jia-Hao Dai ◽  
An-Qi Hu ◽  
Jia-Shuo Zhang ◽  
Wen-Hai Liao ◽  
Hua-Yan Ma ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Eucalyptus Grandis ◽  
Nuclear Factor ◽  
Nuclear Factor Y ◽  
Gene Structures ◽  
Genetic Structures ◽  
Y Family

The transcription factor NF-YB (nuclear factor-YB) family is a subfamily of the nuclear factor Y (NF-Y), which plays an important role in regulating plant growth, development and participates in various stress responses. Although the NF-Y family has been studied in many species, it is still obscure in Eucalyptus grandis. In this study, 23 EgNF-YB genes in eucalyptus were identified and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed the EgNF-YB genes were divided into two clades, LEC-1 type and non-LEC1 type. The evolution of distinct clades was relatively conservative, the gene structures were analogous, and the differences of genetic structures among clades were small. The expression profiles showed that the distinct EgNF-YB genes were highly expressed in diverse tissues, and EgNF-YB4/6/13/19/23 functioned in response to salinity, heat and cold stresses. Our study characterized the phylogenetic relationship, gene structures and expression patterns of EgNF-YB gene family and investigated their potential roles in abiotic stress responses, which provides solid foundations for further functional analysis of NF-YB genes in eucalyptus.

scholarly journals Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

2021 ◽  
Vol 22 (19) ◽  
pp. 10354
Author(s):  
Xinrui Zheng ◽  
Hao Zhang ◽  
Limei Zhang ◽  
Fangsen Xu ◽  
Lei Shi ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Functional Study ◽  
Nuclear Factor ◽  
Nutrient Deficiencies ◽  
Abiotic Stress Response ◽  
Nuclear Factor Y ◽  
Homologous Genes ◽  
Y Family

Nuclear Factor-Y (NF-Y) transcription factors play vital roles in plant abiotic stress response. Here, the NF-Y family in Brassica napus, which is hyper-sensitive to nitrogen (N) deprivation, was comprehensively identified and systematically characterized. A total of 108 NF-Y family members were identified in B. napus and categorized into three subfamilies (38 NF-YA, 46 NF-YB and 24 NF-YC; part of the Arabidopsis NF-YC homologous genes had been lost during B. napus evolution). In addition, the expansion of the NF-Y family in B. napus was driven by whole-genome duplication and segmental duplication. Differed expression patterns of BnaNF-Ys were observed in response to multiple nutrient starvations. Thirty-four genes were regulated only in one nutrient deficient condition. Moreover, more BnaNF-YA genes were differentially expressed under nutrient limited environments compared to the BnaNF-YB and BnaNF-YC subfamilies. Sixteen hub genes responded diversely to N deprivation in five rapeseed tissues. In summary, our results laid a theoretical foundation for the follow-up functional study of the key NF-Y genes in B. napus in regulating nutrient homeostasis, especially N.

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

scholarly journals Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

PLoS ONE ◽  
2019 ◽  
Vol 14 (9) ◽  
pp. e0222203 ◽  
Author(s):  
P. Maheshwari ◽  
Divya Kummari ◽  
Sudhakar Reddy Palakolanu ◽  
U. Nagasai Tejaswi ◽  
M. Nagaraju ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Expression Profile ◽  
Profile Analysis ◽  
Nuclear Factor ◽  
Nuclear Factor Y ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Y Family ◽  
Sorghum Bicolor L

scholarly journals Alcohol dehydrogenase (ADH) genes family in wheat (Triticum aestivum): Genome-wide identification, characterization, phylogenetic relationship and expression patterns

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan ◽  
Xingqi Ou
Keyword(s):  
Abiotic Stress ◽  
Alcohol Dehydrogenase ◽  
Expression Patterns ◽  
Rice Genome ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Wheat Genome ◽  
Element Analysis ◽  
Gene Pairs ◽  
Adh Genes

Abstract Background Alcohol dehydrogenase (ADH) plays important roles in plant survival under anaerobic conditions. Although some research has been carried out the functions of ADH in other plants, that of wheat TaADH family genes in response to abiotic stress are unclear. Results A total of 22 ADH genes were obtained from 14 chromosomes of the wheat genome by systematic screening. Multiple sequence alignment and evolutionary relationship show that these genes contain the characteristics of GroES-like domain and Zinc-binding domain, and these belong to Medium-chain -ADH type and can be divided into three subfamilies. There are 17 pairs of fragment replication genes among TaADH family members in the wheat genome, while there are 9 pairs of collinear gene pairs from ADH family members between wheat and rice genome. We speculate that these fragment repetition events may be the main reason for the amplification of TaADH family genes. Ka/Ks analysis indicated that there were 64 repetitive gene pairs, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these sequences of TaADH gene were relatively conservative and did not change greatly in the process of evolution. Promoter element analysis showed that almost all of the upstream promoters of these genes contained the responsive anaerobic inducible element. Tissue localized expression and expression patterns also demonstrated that the TaADH genes responded to abiotic stress and may play an important role in waterlogging stress during the seed germination stage. Conclusions The results of this study may be helpful to further study the function of TaADH genes and determine the candidate gene for wheat stress resistance breeding.

scholarly journals Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11939
Author(s):  
Jiali Zhao ◽  
Hongyou Li ◽  
Juan Huang ◽  
Taoxiong Shi ◽  
Ziye Meng ◽  
...  
Keyword(s):  
Growth And Development ◽  
Environmental Changes ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Tartary Buckwheat ◽  
Chromosome 6 ◽  
Fagopyrum Tataricum ◽  
Conserved Motifs ◽  
Genome Wide ◽  
Gene Structures

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

scholarly journals In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 236 ◽  
Author(s):  
Lianghai Chen ◽  
Yong Zhou ◽  
Wei Lai ◽  
Lifang Hu ◽  
Lunwei Jiang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Crop Improvement ◽  
Nuclear Factor ◽  
Rna Seq ◽  
Abiotic Stress Response ◽  
Promoter Regions ◽  
Nuclear Factor Y ◽  
Cucumber Genome ◽  
Drought And Salt Stress ◽  
Gene Structures

The nuclear factor Y (NF-Y) transcription factors (TFs) play vital regulatory roles in diverse developmental processes and responses to abiotic stresses in plants. However, the NF-Y genes remain largely unknown in cucumber. In this study, based on phylogenetic and protein structure analyses, we identified 27 CsaNF-Y members of this gene family in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs. Their chromosome locations, gene structures, conserved domains, gene duplication, and promoter regions containing stress- and hormone-responsive cis-elements were also analyzed. As reported earlier, RNA-seq data showed that the expression of some CsaNF-Y genes was tissue-specific and varied during fruit development. The qRT-PCR results showed that all the detected CsaNF-Y genes were differentially regulated by drought and salt stress. Taken together, our findings provide a comprehensive understanding of CsaNF-Y genes in the development and abiotic stress response of cucumber and lay the foundation for future crop improvement.

scholarly journals Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

2020 ◽  
Author(s):  
Jingping Yuan ◽  
Changwei Shen ◽  
Jingjing Xin ◽  
Zhenxia Li ◽  
Xinzheng Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Element Analysis ◽  
Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

scholarly journals Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1763 ◽  
Author(s):  
Abdullah Shalmani ◽  
Sheng Fan ◽  
Peng Jia ◽  
Guofang Li ◽  
Izhar Muhammad ◽  
...  
Keyword(s):  
Gene Family ◽  
Malus Domestica ◽  
Growth And Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Structural Features ◽  
Flower Induction ◽  
Specific Expression ◽  
Flowering Induction

BBX proteins play important roles in regulating plant growth and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses. At present, the genomes of seven Rosacea fruit species have been fully sequenced. However, little is known about the BBX gene family and their evolutionary history in these Rosacea species. Therefore, in this study total, 212 BBX genes were investigated from seven Rosacea species (67 from Malus × domestica, 40 from Pyruscommunis, 22 from Rosa Chinesis, 20 from Prunuspersica, 21 from Fragariavesca, 22 from Prunusavium, and 20 from Rubusoccidentalis). The chemical properties, gene structures, and evolutionary relationships of the BBX genes were also studied. All the BBX genes were grouped into six subfamilies on the basis of their phylogenetic relationships and structural features. Analysis of gene structure, segmental and tandem duplication, gene phylogeny, and tissue-specific expression with the ArrayExpress database showed their diversification in function, quantity, and structure. The expression profiles of 19 MdBBX genes in different tissues were evaluated through qRT-PCR. These genes showed distinct transcription level among the tested tissues (bud, flower, fruit, stem, and leaf). Moreover, expression patterns of 19 MdBBX genes were examined during flowering induction time under flowering-related hormones and treatments (GA3, 6-BA, and sucrose). The expressions of the candidates BBX genes were affected and showed diverse expression profile. Furthermore, changes in response to these flowering-related hormones and treatment specifying their potential involvement in flowering induction. Based on these findings, BBX genes could be used as potential genetic markers for the growth and development of plants particularly in the area of functional analysis, and their involvement in flower induction in fruit plants.

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