scholarly journals Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10483
Author(s):  
Lei Dong ◽  
Yue Lu ◽  
Shubing Liu
Keyword(s):  
Seed Germination ◽  
Common Wheat ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Triticum Dicoccoides ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Group 2

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

scholarly journals Genome-Wide Identification and Expression Profiling Analysis of WOX Family Proteins Encoded Genes in Triticeae Plant Species

2020 ◽  
Author(s):  
Lei Shi ◽  
Ke Wang ◽  
Lipu Du ◽  
Yuxia Song ◽  
Huihui Li ◽  
...  
Keyword(s):  
Plant Regeneration ◽  
Plant Species ◽  
Triticum Turgidum ◽  
Baby Boom ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Family Members ◽  
Triticum Dicoccoides ◽  
Substitution Lines ◽  
Specific Pcr

Abstract Background: Genotype dependence of plant regeneration is an important factor restricting the genetic improvement of Triticeae plant species. The WUSCHEL-related homeobox (WOX) is a group of plant specific transcription factor, which play an important role in plant growth and development, and cell division and differentiation. Recent studies revealed that the application of regeneration-related genes such as WOX and BABY BOOM (BBM) could improve plant regeneration. The application of WOX genes is one of the ways to improve the genetic transformation system of Triticeae and other species, but there are rare studies in this area.Results: From the available genome sequence database, in total 136 WOX transcripts were identified for the Triticeae plants, including 43 in Triticum aestivum, 30 in Triticum turgidum, 25 in Triticum dicoccoides, 17 in Hordeum vulgare, 13 in Aegilops tauschii, and 8 in Triticum urartu. All of the WOX family genes were distributed on the chromosomes of homologous groups 1 to 5 in the six Triticeae species, part of which were confirmed by their specific PCR markers using a set of T. durum-T. aestivum genome D substitution lines. All of the WOX proteins in the six Triticeae species could be grouped into three clades, similar to those in rice (Oryza sativa L.) and Arabidopsis. WOX family members were conserved among these Triticeae plants, all of them contained the conserved HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS motif, while only TaWUS and TaWOX9 in all the six Triticeae plant species contained the ERF-associated amphiphilic repression (EAR) motif. The expression profiles of TaWOX genes by quantitative real-time PCR (qPCR) showed obvious difference among WOX family members.Conclusions: Totally 130 WOX genes were identified in the six Triticeae plant species. The WOX family genes were located on the chromosomes in the five homologous groups except groups 6 and 7 in the Triticeae species, and their expression profiles were different in different tissues, indicating that each of them had diverse function. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae plant species.

scholarly journals Long non-coding RNAs in wild wheat progenitors

2018 ◽  
Author(s):  
Alice Pieri ◽  
Mario Enrico Pè ◽  
Edoardo Bertolini
Keyword(s):  
Aegilops Tauschii ◽  
Noncoding Rnas ◽  
Reproductive Organs ◽  
Long Noncoding Rnas ◽  
D Genome ◽  
Specific Expression ◽  
Wild Wheat ◽  
Organ Specific ◽  
Species Specific ◽  
And Function

AbstractTriticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona-fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

scholarly journals Region-specific expression of androgen and growth factor pathway genes in the rat epididymis and the effects of dual 5α-reductase inhibition

2006 ◽  
Vol 190 (3) ◽  
pp. 779-791 ◽  
Author(s):  
Natali Anne Henderson ◽  
Gerard M Cooke ◽  
Bernard Robaire
Keyword(s):  
Gene Expression ◽  
Androgen Receptor ◽  
Expression Profiles ◽  
Gene Array ◽  
Sperm Maturation ◽  
Male Rats ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Signaling Systems ◽  
Reductase Inhibitors

Dihydrotestosterone (DHT) is the primary androgen acting in the epididymis, the site of sperm maturation. Previously, we showed that the treatment of male rats with PNU157706, an inhibitor that acts on both isoforms of 5α-reductase to prevent DHT formation, has effects on the expression of genes implicated in processes that create the optimal luminal microenvironment required for sperm maturation, and on sperm maturation itself. However, signaling pathways involved in regulating or mediating DHT actions in the epididymis remain largely unknown. The goals of this study were to determine the expression profiles of potential signaling systems in the epididymis and assess their DHT-dependence using two different dual 5α-reductase inhibitors. Rats were untreated or gavaged with vehicle, 10 mg/kg per day PNU157706 or 32 mg/kg per day FK143 for 28 days and epididymal gene expression was analyzed. Gene array analysis revealed analogous effects of FK143 on overall epididymal gene expression when compared with previous PNU157706 studies. Quantitative RT-PCR analysis of the expression of the 5α-reductase isozymes, androgen receptor, and members of the IGF, FGF, TGF, and VEGF families revealed novel region-specific expression profiles in the epididymis that were differentially affected by 5α-reductase inhibition; the two inhibitors had parallel effects. Specifically, in proximal regions, 5α-reductase 1, androgen receptor, and TGF-β1 expression increased after treatment, while in distal regions expression of IGF-I, IGFBP-5, IGFBP-6, and FGF-10 decreased. These results provide insight into epididymal signaling mechanisms and indicate potential candidates acting either upstream or downstream of DHT to regulate and/or mediate its actions in the epididymis.

scholarly journals Genome-Wide Investigation of Spliceosomal SM/LSM Genes in Wheat (Triticum aestivum L.) and Its Progenitors

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1429
Author(s):  
Ruiting Gao ◽  
Ning Su ◽  
Wenqiu Pan ◽  
Qiaoyu Bao ◽  
Zhen Li ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Aegilops Tauschii ◽  
Enrichment Analysis ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Triticum Dicoccoides ◽  
Regulatory Elements ◽  
Salt Tolerance Gene

The SSM/SLSM (spliceosomal Smith (SM)/SM-like (LSM)) genes are the central components of the spliceosome in eukaryotes, which play an important role in regulating RNA splicing, participating in diverse biological processes. Although it has been detected in Arabidopsis and rice etc. plants, the members and significance of the SSM/SLSM gene family in wheat are still not reported. In this study, we identified the SSM/SLSM genes in wheat and its progenitors at genome-scale, where 57 SSM/SLSM genes were identified in wheat, together with 41, 17and 19 found in Triticum dicoccoides, Triticum urartu, and Aegilops tauschii. Furthermore, their phylogenetic relationship, gene structures, conserved motifs, and cis-regulatory elements were systematically analyzed. By synteny analysis, good collinearity of SSM/SLSM genes was found among bread wheat and its progenitors’ genomes, and the distribution of SMD2 genes in wheat chromosome 5A, 4B and 4D located in the 4AL-5AL-7BS chromosome model, due to the translocation. Then, the positively selected genes were further investigated based on the non-synonymous to synonymous (dN/dS) analysis of the orthologous pairs. Finally, the expression profiles of the SSM/SLSM genes were detected using RNA-seq datasets, and eight stress-responsive candidate genes were selected to validate their expression through qPCR (real-time quantitative polymerase chain reaction). According to the co-expression network analysis, the correlation between the LSM7-7A gene and related genes was illustrated through Gene Ontology (GO) enrichment analysis. Furthermore, the LSM7-7A gene was related to the Arabidopsis homologous salt tolerance gene RCY1. This investigation systematically identified the complete candidates of SSM/SLSM genes and their characters in wheat and its progenitors, and provided clues to a better understanding of their contribution during the wheat polyploidy process.

scholarly journals Mummichog gill and operculum exhibit functionally consistent claudin-10 paralog profiles and Claudin-10c hypersaline response

Biology Open ◽  
2021 ◽  
Author(s):  
Chun Chih Chen ◽  
William S. Marshall ◽  
George N. Robertson ◽  
Regina R.F. Cozzi ◽  
Scott P. Kelly
Keyword(s):  
Fundulus Heteroclitus ◽  
Sea Water ◽  
Expression Profiles ◽  
Protein Abundance ◽  
Transmembrane Conductance Regulator ◽  
The Novel ◽  
Specific Expression ◽  
Secretion Pathway ◽  
Organ Specific ◽  
Organ Specific Expression

Claudin (Cldn) -10 tight junction (TJ) proteins are hypothesized to form the paracellular Na+ secretion pathway of hyposmoregulating mummichog (Fundulus heteroclitus) branchial epithelia. Organ-specific expression profiles showed that only branchial organs (the gill and opercular epithelium, OE) exhibited abundant cldn-10 paralog transcripts, which typically increased following sea water (SW) to hypersaline (2SW) challenge. Post-translational properties, protein abundance, and ionocyte localization of Cldn-10c, were then examined in gill and OE. Western blot analysis revealed two Cldn-10c immunoreactive bands in the mummichog gill and OE at ∼29 kDa and ∼40 kDa. The heavier protein could be eliminated by glycosidase treatment, demonstrating the novel presence of a glycosylated Cldn-10c. Protein abundance of Cldn-10c increased in gill and OE of 2SW-exposed fish. Cldn-10c localized to the sides of gill and OE ionocyte apical crypts and partially colocalized with cystic fibrosis transmembrane conductance regulator and F-actin, consistent with TJ complex localization. Cldn-10c immunofluorescent intensity increased but localization was unaltered by 2SW conditions. In support of our hypothesis, cldn-10/Cldn-10 TJ protein dynamics in gill and OE of mummichogs and TJ localization are functionally consistent with the creation and maintenance of salinity-responsive, cation-selective pores that facilitate Na+ secretion in hyperosmotic environments.

scholarly journals Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus

2022 ◽  
Vol 12 ◽  
Author(s):  
Rehman Sarwar ◽  
Rui Geng ◽  
Lei Li ◽  
Yue Shan ◽  
Ke-Ming Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Future Research ◽  
Plant Tolerance ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Duplication Events

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.

scholarly journals The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis

2019 ◽  
Vol 20 (5) ◽  
pp. 371-388
Author(s):  
Songfeng Xie ◽  
Licao Cui ◽  
Xiaole Lei ◽  
Guang Yang ◽  
Jun Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Aegilops Tauschii ◽  
Vital Role ◽  
Pcr Analysis ◽  
Protein Motif ◽  
Genome Wide ◽  
A Genome ◽  
As Stress

Background: The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat. Objective: To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and its two progenitors using updated genome information provided here. Results: In total, 63, 13 and 17 TIFY proteins were identified in wheat, Triticum urartu and Aegilops tauschii respectively. Phylogenetic analysis clustered them into 18 groups with 14 groups possessing A, B and D copies in wheat, demonstrating the completion of the genome as well as the two rounds of allopolyploidization events. Gene structure, conserved protein motif and cis-regulatory element divergence of A, B, D homoeologous copies were also investigated to gain insight into the evolutionary conservation and divergence of homoeologous genes. Furthermore, the expression profiles of the genes were detected using the available RNA-seq and the expression of 4 drought-responsive candidates was further validated through qRT-PCR analysis. Finally, the co-expression network was constructed and a total of 22 nodes with 121 edges of gene pairs were found. Conclusion: This study systematically reported the characteristics of the wheat TIFY family, which ultimately provided important targets for further functional analysis and also facilitated the elucidation of the evolution mechanism of TIFY genes in wheat and more.

scholarly journals Different Functions and Expression Profiles of Curcin and Curcin-L in Jatropha curcas L.

2010 ◽  
Vol 65 (5-6) ◽  
pp. 355-362 ◽  
Author(s):  
Xiaobo Qin ◽  
Caixia Shao ◽  
Pei Hou ◽  
Jihai Gao ◽  
Ningfei Lei ◽  
...  
Keyword(s):  
Jatropha Curcas ◽  
Expression Profiles ◽  
Mature Embryo ◽  
Amino Acid Sequences ◽  
Specific Expression ◽  
Protein Levels ◽  
Organ Specific ◽  
Flanking Region ◽  
Specific Expression Pattern ◽  
High And Low Temperatures

To date, two types of ribosome-inactivating proteins (RIPs) have been found in Jatropha curcas. One is curcin, which has been isolated from the endosperm, and the other is curcin-L, which is expressed in leaves upon stress treatment. Phylogenetic analysis of the predicted amino acid sequences of the RIPs in plants revealed that these belong to a major subfamily and are close to trichosanthin (TCS). Studies on the mRNA and protein levels showed that both curcin and curcin-L have an organ-specific expression pattern. Curcin is only expressed and accumulated in the endosperm; its expression begins in the globular embryo period and peaks during the mature embryo period. In contrast, curcin-L is only expressed in the leaves, but its expression is induced by certain conditions such as treatment with phytohormones or polyethylene glycol, exposure to high and low temperatures, and fungal infection. Analysis of the 5’ flanking regions of curcin and curcin-L revealed that the 5’ flanking region of curcin-L has three major inserted fragments, which are not present in the corresponding region of curcin. Comparison of characteristic cis-elements suggests the presence of several motifs that are involved in the endosperm-specific expression in the 5’ flanking region of curcin, while in curcin-L some stress- and defense-responsive motifs are found to be mainly located in the three inserted fragments. Comparison of the antifungal activity of the two RIPs showed that the one of curcin-L is higher than that of curcin. Differences in the expression and activity of curcin and curcin-L suggest that these two RIPs have different functions.

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