scholarly journals Comparative Analysis of the aquaporin Gene Family in 12 Fish Species

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 233 ◽  
Author(s):  
Jun Cao ◽  
Feng Shi
Keyword(s):  
Comparative Analysis ◽  
Gene Family ◽  
Fish Species ◽  
Expression Profiles ◽  
Water Channel ◽  
Organophosphorus Pesticide ◽  
Gene Organization ◽  
Pesticide Stress ◽  
Aquaporin Gene ◽  
The Stability

Aquaporins (Aqps) are a class of water channel proteins that play key roles in many physiological functions and cellular processes. Here, we analyzed 166 putative Aqp genes in 12 fish species and divided them into four groups. Gene organization and motif distribution analyses suggested potentially conserved functions in each group. Several recombination events were identified in some members, which accelerate their divergence in evolution. Furthermore, a few positive selection sites were identified, and mutations at these sites could alter the stability of Aqp proteins. In addition, expression profiles of some Aqp genes under pathogen infection and organophosphorus pesticide stress were also investigated. The result implied that several Aqp genes may affect different immune responses and osmoregulation. This study provides a comparative analysis of the fish Aqp gene family to facilitate further functional analyses.

scholarly journals Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit

2021 ◽  
Vol 22 (22) ◽  
pp. 12492
Author(s):  
Muhammad Aamir Manzoor ◽  
Irfan Ali Sabir ◽  
Iftikhar Hussain Shah ◽  
Han Wang ◽  
Zhao Yu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Comparative Analysis ◽  
Gene Family ◽  
Prunus Persica ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Composition Analysis ◽  
Rosaceae Species ◽  
Gata Transcription Factors ◽  
Gata Gene

The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.

scholarly journals Identification of Aquaporin Gene Family in Response to Natural Cold Stress in Ligustrum × Vicaryi Rehd.

2021 ◽  
Author(s):  
Jiahui Dong ◽  
Shance Niu ◽  
Juan Zhou ◽  
Ji Qian ◽  
Mengnan Zhao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Theoretical Basis ◽  
Cold Resistance ◽  
Expression Profiles ◽  
Resistance Breeding ◽  
Temperature Growth ◽  
Genome Wide ◽  
Aquaporin Gene ◽  
Genes Expression

Abstract Background: Maintaining water balance in various adversities is a difficult and critical challenge for plants. Studies have shown that aquaporins located on cytomembrane play an important role in maintaining water homeostasis under various environmental stresses. Some studies have shown that aquaporins are involved in the tolerance mechanism of plant cells under cold stress, and the aquaporin gene family is closely related to the cold resistance of plants. Ligustrum × vicaryi Rehd. plays a significant role in urban landscaping with poor cold resistance at the seedling stage and early planting stage. Screening the target aquaporin genes of Ligustrum × vicaryi related to cold resistance during natural cold stress will provide a scientific theoretical basis for cold resistance breeding of Ligustrum × vicaryi.Results: In this study, the genome-wide identification of the aquaporin gene family was performed at four different overwintering periods in September, November, January and April, and finally 58 candidate Ligustrum × vicaryi aquaporin (LvAQP) genes were identified. The phylogenetic analysis revealed that four subfamilies of the LvAQP gene family: 32 PIPs, 11 TIPs, 11 NIPs, and 4 SIPs, among which there were more genes in the PIPs subfamily than that in other plants. The key LvAQP genes were found through analyzing aquaporin genes related to cold stress in other plants and LvAQP genes expression profiles. The up-regulated key LvAQP genes were Cluster-9981.114831, Cluster-9981.104986, and Cluster-9981.120365, and the down-regulated key LvAQP genes were Cluster-9981.112839, Cluster-9981.109034, Cluster-9981.89369, Cluster-9981.110451, Cluster-9981.107281, Cluster-9981.112777, Cluster-9981.112789, Cluster-9981.122691 and Cluster-9981.88037. These genes play a key role related to cold tolerance in the nature low temperature growth stage of Ligustrum × vicaryi. Conclusions: This study systematically identified the AQP gene family in Ligustrum × vicaryi and screened for 20 differential expression LvAQP genes related to cold stress, among which 11 genes belonged to PIPs subfamily. The results of this research will lay the foundation for further biological function verification of cold resistance-related aquaporin candidate genes in Ligustrum × vicaryi, especially PIPs subfamily, and provide theoretical basis and technical support for improving seedling quality and breeding.

Functional analysis of the aquaporin gene family in Caenorhabditis elegans

2007 ◽  
Vol 292 (5) ◽  
pp. C1867-C1873 ◽  
Author(s):  
Chunyi George Huang ◽  
Todd Lamitina ◽  
Peter Agre ◽  
Kevin Strange
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Family ◽  
Fluorescent Protein ◽  
Water Channel ◽  
Cell Types ◽  
Culture Conditions ◽  
C Elegans ◽  
Hypotonic Stress ◽  
Aquaporin Gene ◽  
Green Fluorescent

Aquaporin channels facilitate the transport of water, glycerol, and other small solutes across cell membranes. The physiological roles of many aquaporins remain unclear. To better understand aquaporin function, we characterized the aquaporin gene family in the nematode Caenorhabditis elegans. Eight canonical aquaporin-encoding genes ( aqp) are present in the worm genome. Expression of aqp-2, aqp-3, aqp-4, aqp-6, or aqp-7 in Xenopus oocytes increased water permeability five- to sevenfold. Glycerol permeability was increased three to sevenfold by expression of aqp-1, aqp-3, or aqp-7. Green fluorescent protein transcriptional and translational reporters demonstrated that aqp genes are expressed in numerous C. elegans cell types, including the intestine, excretory cell, and hypodermis, which play important roles in whole animal osmoregulation. To define the role of C. elegans aquaporins in osmotic homeostasis, we isolated deletion alleles for four aqp genes, aqp-2, aqp-3, aqp-4, and aqp-8, which are expressed in osmoregulatory tissues and mediate water transport. Single, double, triple, and quadruple aqp mutant animals exhibited normal survival, development, growth, fertility, and movement under normal and hypertonic culture conditions. aqp-2; aqp-3; aqp-4; aqp-8 quadruple mutants exhibited a slight defect in recovery from hypotonic stress but survived hypotonic stress as well as wild-type animals. These results suggest that C. elegans aquaporins are not essential for whole animal osmoregulation and/or that deletion of aquaporin genes activates mechanisms that compensate for loss of water channel function.

scholarly journals Genome-Wide Identification of Aquaporin Gene Family in Pitaya Reveals an HuNIP6;1 Involved in Flowering Process

2021 ◽  
Vol 22 (14) ◽  
pp. 7689
Author(s):  
Xiaoying Ye ◽  
Yongshun Gao ◽  
Canbin Chen ◽  
Fangfang Xie ◽  
Qingzhu Hua ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Circadian Rhythm ◽  
Gene Family ◽  
Expression Profiles ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Aquaporin Gene ◽  
Key Genes ◽  
Stomata Movement ◽  
Flowering Process

Aquaporins (AQPs) are essential membrane proteins involved in seed maturation and germination, stomata movement, photosynthesis, and regulation of plant flowering processes. Pitaya flowers are open at night and wither at daybreak, which shows an obvious circadian rhythm. In this study, a comprehensive genome-wide analysis of AQPs in Hylocereus undantus was conducted to screen key genes associated with flowering processes. A total of 33 HuAQP genes were identified from the H. undantus genome. The 33 HuAQPs were grouped into four subfamilies: 10 PIPs, 13 TIPs, 8 NIPs, and 2 SIPs, which were distributed on 9 out of 11 pitaya chromosomes (Chr) (except for Chr7 and Chr10). Results from expression profiles showed that HuNIP6;1 may be involved in pitaya’s floral opening. HuNIP6;1 was localized exclusively in the cell membrane. Overexpression of HuNIP6;1 in Arabidopsis thaliana significantly promoted early flowering through regulating negative flowering regulators of MJM30, COL9, and PRR5, suggesting that HuNIP6;1 plays key roles in regulating flowering time. The present study provides the first genome-wide analysis of the AQP gene family in pitaya and valuable information for utilization of HuAQPs.

scholarly journals Gene Structures, Evolution, Classification and Expression Profiles of the Aquaporin Gene Family in Castor Bean (Ricinus communis L.)

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0141022 ◽  
Author(s):  
Zhi Zou ◽  
Jun Gong ◽  
Qixing Huang ◽  
Yeyong Mo ◽  
Lifu Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Castor Bean ◽  
Ricinus Communis ◽  
Expression Profiles ◽  
Ricinus Communis L ◽  
Aquaporin Gene ◽  
Gene Structures

scholarly journals Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

2020 ◽  
Vol 22 (1) ◽  
pp. 253
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Functional Groups ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Crop Improvement ◽  
Potato Virus X ◽  
Tissue Growth ◽  
Abiotic Stress Response ◽  
Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

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