scholarly journals Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9225
Author(s):  
Yaoyao Jiang ◽  
Haichao Hu ◽  
Yuhua Ma ◽  
Junliang Zhou
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Evolutionary Analysis ◽  
Biotic And Abiotic Stress ◽  
Bioinformatic Tools ◽  
Genome Wide ◽  
Specific Analysis

Background The fibrillin (FBN) gene family is highly conserved and widely distributed in the photosynthetic organs of plants. Members of this gene family are involved in the growth and development of plants and their response to biotic and abiotic stresses. Wheat (Triticum aestivum), an important food crop, has a complex genetic background and little progress has occurred in the understanding of its molecular mechanisms. Methods In this study, we identified 26 FBN genes in the whole genome of T. aestivum through bioinformatic tools and biotechnological means. These genes were divided into 11 subgroups and were distributed on 11 chromosomes of T. aestivum. Interestingly, most of the TaFBN genes were located on the chromosomes 2A, 2B and 2D. The gene structure of each subgroup of gene family members and the position and number of motifs were highly similar. Results The evolutionary analysis results indicated that the affinities of FBNs in monocots were closer together. The tissue-specific analysis revealed that TaFBN genes were expressed in different tissues and developmental stages. In addition, some TaFBNs were involved in one or more biotic and abiotic stress responses. These results provide a basis for further study of the biological function of FBNs.

scholarly journals Genome-Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

2016 ◽  
Vol 17 (7) ◽  
pp. 1004 ◽  
Author(s):  
Wei Xu ◽  
Zexi Chen ◽  
Naeem Ahmed ◽  
Bing Han ◽  
Qinghua Cui ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Gras Gene

scholarly journals Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

2018 ◽  
Author(s):  
Guodong Chen ◽  
Xiaolong Li ◽  
Xin qiao ◽  
Jiaming Li ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Higher Plants ◽  
Chloride Transport ◽  
Structural Characteristics ◽  
Evolutionary Analysis ◽  
Anion Channels ◽  
Genome Wide ◽  
A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

scholarly journals Genome-wide identification and comparative analysis of Dof gene family in Brassica napus

2020 ◽  
Author(s):  
Neeta Lohani ◽  
Saeid Babaei ◽  
Mohan B. Singh ◽  
Prem L. Bhalla
Keyword(s):  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Stress Responses ◽  
Structure Evolution ◽  
Oilseed Crop ◽  
Evolutionary Analysis ◽  
Abiotic Stress Response ◽  
Protein Motifs ◽  
Genome Wide

AbstractDOF, DNA binding with one finger proteins are plant-specific transcription factors shown to play roles in diverse plant functions. However, a—little is known about DOF protein repertoire of the allopolyploid crop, Brassica napus. Here, we report genome-wide identification and systematic analysis of the Dof transcription factor family in this important oilseed crop. We identified 117 Brassica napus Dof genes (BnaDofs). So far, this is the largest number of Dof genes reported in a single eudicot species. Based on phylogenetic analysis, BnaDofs were classified into nine groups (A, B1, B2. C1, C2.1, C2.2, C3, D1, D2). Most members belonging to a particular group displayed conserved gene structural organisation and similar protein motifs distribution. Chromosomal localisation analysis highlighted the uneven distribution of BnaDofs across all chromosomes. Evolutionary analysis exemplified that the divergence of Brassica genus from Arabidopsis, the whole genome triplication event, and the hybridisation of B. oleracea and B. rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of Dof TF gene family in B. napus. Functional annotation of BnaDof proteins, cis-element analysis of their promoters suggested potential roles in organ development, the transition from vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness as well as abiotic stress responses. Furthermore, the transcriptomic analysis highlighted the preferential tissue-specific expression patters of BnaDofs and their role in response to various abiotic stress. Overall, this study provides a comprehensive understanding of the molecular structure, evolution, and potential functional roles of Dof genes in plant development and abiotic stress response.

scholarly journals Genome-Wide Identification of Triticum aestivum Xylanase Inhibitor Gene Family and Inhibitory Effects of XI-2 Subfamily Proteins on Fusarium graminearum GH11 Xylanase

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Liu ◽  
Nannan Han ◽  
Sheng Wang ◽  
Can Chen ◽  
Jie Lu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Fusarium Graminearum ◽  
Stress Responses ◽  
Developmental Stages ◽  
Resistance Breeding ◽  
Homologous Gene ◽  
Genome Database ◽  
Xylanase Inhibitor ◽  
Six Genes

Triticum aestivum xylanase inhibitor (TaXI) gene plays an important role in plant defense. Recently, TaXI–III inhibitor has been shown to play a dual role in wheat resistance to Fusarium graminearum infection. Thus, identifying the members of the TaXI gene family and clarifying its role in wheat resistance to stresses are essential for wheat resistance breeding. However, to date, no comprehensive research on TaXIs in wheat (Triticum aestivum L.) has been conducted. In this study, a total of 277 TaXI genes, including six genes that we cloned, were identified from the recently released wheat genome database (IWGSC RefSeq v1.1), which were unevenly located on 21 chromosomes of wheat. Phylogenetic analysis divided these genes into six subfamilies, all the six genes we cloned belonged to XI-2 subfamily. The exon/intron structure of most TaXI genes and the conserved motifs of proteins in the same subfamily are similar. The TaXI gene family contains 92 homologous gene pairs or clusters, 63 and 193 genes were identified as tandem replication and segmentally duplicated genes, respectively. Analysis of the cis-acting elements in the promoter of TaXI genes showed that they are involved in wheat growth, hormone-mediated signal transduction, and response to biotic and abiotic stresses. RNA-seq data analysis revealed that TaXI genes exhibited expression preference or specificity in different organs and developmental stages, as well as in diverse stress responses, which can be regulated or induced by a variety of plant hormones and stresses. In addition, the qRT-PCR data and heterologous expression analysis of six TaXI genes revealed that the genes of XI-2 subfamily have double inhibitory effect on GH11 xylanase of F. graminearum, suggesting their potential important roles in wheat resistance to F. graminearum infection. The outcomes of this study not only enhance our understanding of the TaXI gene family in wheat, but also help us to screen more candidate genes for further exploring resistance mechanism in wheat.

scholarly journals Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shutao He ◽  
Xiaomeng Hao ◽  
Shuli He ◽  
Xiaoge Hao ◽  
Xiaonan Chen
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Sweet Potato ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Promoters ◽  
Biotic And Abiotic Stress ◽  
Protein Motifs ◽  
Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

scholarly journals Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

2021 ◽  
Vol 22 (22) ◽  
pp. 12414
Author(s):  
Xiang Li ◽  
Kewei Cai ◽  
Xiaona Pei ◽  
Yan Li ◽  
Yanbo Hu ◽  
...  
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Developmental Stages ◽  
Mature Stage ◽  
Juglans Mandshurica ◽  
Genome Wide ◽  
Specific Analysis ◽  
Fruit Development And Ripening ◽  
Nac Gene Family ◽  
Regulatory Functions

The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family.

scholarly journals Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12491
Author(s):  
Xianwen Meng ◽  
Jing Liu ◽  
Mingde Zhao
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Linum Usitatissimum ◽  
Ring Finger ◽  
Synonymous Substitution ◽  
Segmental Duplications ◽  
Biotic And Abiotic Stress ◽  
Gene Pairs ◽  
Genome Wide ◽  
Substitution Ratio

Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.

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