Genome-wide Characterization of Major Intrinsic Protein (MIP) Gene Family in Brachypodium distachyon

2018 ◽  
Vol 13 (5) ◽  
pp. 536-552 ◽  
Author(s):  
Ankush Ashok Saddhe ◽  
Shweta ◽  
Kareem A. Mosa ◽  
Kundan Kumar ◽  
Manoj Prasad ◽  
...  
Keyword(s):  
Gene Family ◽  
Brachypodium Distachyon ◽  
Major Intrinsic Protein ◽  
Intrinsic Protein ◽  
Genome Wide

scholarly journals Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice

2020 ◽  
Vol 16 ◽  
pp. 117693432094149
Author(s):  
Jun Yang ◽  
Peng Xu ◽  
Diqiu Yu
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Japonica Rice ◽  
Segmental Duplications ◽  
Related Sequence ◽  
Genome Wide ◽  
A Genome

Rice ( Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.

Genome-wide analysis of SnRK gene family in Brachypodium distachyon and functional characterization of BdSnRK2.9

Plant Science ◽  
2015 ◽  
Vol 237 ◽  
pp. 33-45 ◽  
Author(s):  
Lianzhe Wang ◽  
Wei Hu ◽  
Jiutong Sun ◽  
Xiaoyu Liang ◽  
Xiaoyue Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Characterization ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

Genome-wide identification and characterization of the Dof gene family in moso bamboo (Phyllostachys heterocycla var. pubescens)

2016 ◽  
Vol 38 (8) ◽  
pp. 733-745 ◽  
Author(s):  
Tao Wang ◽  
Jin-Jun Yue ◽  
Xue-Ji Wang ◽  
Lu Xu ◽  
Lu-Bin Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Moso Bamboo ◽  
Genome Wide ◽  
Phyllostachys Heterocycla ◽  
Identification And Characterization

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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