scholarly journals Genome-Wide Identification and Expression Analysis of MYB Transcription Factors and Their Responses to Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 97
Author(s):  
Huihui Li ◽  
Yanwei Zhou ◽  
Zongxin Ma ◽  
Xiaoqing Lu ◽  
Yunlong Li ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Fragaria Vesca ◽  
Specific Expression ◽  
Expression Levels ◽  
Woodland Strawberry ◽  
Organ Specific ◽  
Multiple Treatments ◽  
Myb Genes ◽  
Myb Proteins

Woodland strawberry (Fragaria vesca) is a diploid strawberry that is widely used as a model of cultivated octoploid strawberry (Fragaria × ananassa). It has also been used as a model for Rosaceae fruits, non-climacteric fruits, and stolons. The MYB superfamily is the largest transcription factor family in plants, and its members play important roles in plant growth and development. However, the complete MYB superfamily in woodland strawberry has not been studied. In this study, a total of 217 MYB genes were identified in woodland strawberry and classified into four groups: one 4R-MYB protein, five 3R-MYB proteins, 113 2R-MYB proteins, and 98 1R-MYB proteins. The phylogenetic relationship of each MYB subgroup was consistent in terms of intron/exon structure and conserved motif composition. The MYB genes in woodland strawberry underwent loss and expansion events during evolution. The transcriptome data revealed that most FveMYB genes are expressed in several organs, whereas 15 FveMYB genes exhibit organ-specific expression, including five genes (FveMYB101, -112, -44, and -8; FveMYB1R81) in roots, two genes (FveMYB62 and -77) in stolon tips, three genes (FveMYB99 and -35; FveMYB1R96) in open flowers, and five genes (FveMYB76 and -100; FveMYB1R4, -5, and -86) in immature fruits. During fruit ripening of woodland strawberry, the expression levels of 84 FveMYB genes were decreased, of which five genes (FveMYB4, -22, -50, and -66; FveMYB1R57) decreased more than 10-fold, whereas those 18 FveMYB genes were increased, especially FveMYB10 and FveMYB74 increased more than 30-fold. In addition, the expression levels of 36, 68, 52, and 62 FveMYB genes were altered by gibberellic acid, abscisic acid, cold, and heat treatments, respectively, and among them, several genes exhibited similar expression patterns for multiple treatments, suggesting possible roles in the crosstalk of multiple signaling pathways. This study provides candidate genes for the study of stolon formation, fruit development and ripening, and abiotic stress responses.

scholarly journals Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

2019 ◽  
Vol 20 (18) ◽  
pp. 4593 ◽  
Author(s):  
Hong Chen ◽  
Huihui Li ◽  
Xiaoqing Lu ◽  
Longzheng Chen ◽  
Jing Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fruit Ripening ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Fragaria Vesca ◽  
Motif Analysis ◽  
Specific Expression ◽  
Woodland Strawberry ◽  
Organ Specific

The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA3 treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA3 treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.

scholarly journals BplMYB46 from Betula platyphylla Can Form Homodimers and Heterodimers and Is Involved in Salt and Osmotic Stresses

2019 ◽  
Vol 20 (5) ◽  
pp. 1171 ◽  
Author(s):  
Yan-Min Wang ◽  
Chao Wang ◽  
Hui-Yan Guo ◽  
Yu-Cheng Wang
Keyword(s):  
Stress Responses ◽  
Target Genes ◽  
Expression Patterns ◽  
Betula Platyphylla ◽  
Glucuronidase Activity ◽  
Fluorescence Quantitative Pcr ◽  
Yeast Two Hybrid System ◽  
Myb Genes ◽  
Myb Proteins ◽  
Viral Oncogene Homolog

MYB proteins play important roles in the regulation of plant growth, development, and stress responses. Overexpression of BplMYB46 from Betula platyphylla improved plant salt and osmotic tolerances. In the present study, the interaction of eight avian myeloblastosis viral oncogene homolog (MYB) transcription factors with BplMYB46 was investigated using the yeast two-hybrid system, which showed that BplMYB46 could form homodimers and heterodimers with BplMYB6, BplMYB8, BplMYB11, BplMYB12, and BplMYB13. Relative beta-glucuronidase activity and chromatin immunoprecipitation assays showed that the interaction between BplMYB46 and the five MYBs increased the binding of BplMYB46 to the MYBCORE motif. A subcellular localization study showed that these MYBs were all located in the nucleus. Real-time fluorescence quantitative PCR results indicated that the expressions of BplMYB46 and the five MYB genes could be induced by salt and osmotic stress, and the BplMYB46 and BplMYB13 exhibited the most similar expression patterns. BplMYB46 and BplMYB13 co-overexpression in tobacco using transient transformation technology improved tobacco’s tolerance to salt and osmotic stresses compared with overexpressing BplMYB13 or BplMYB46 alone. Taken together, these results demonstrated that BplMYB46 could interact with five other MYBs to form heterodimers that activate the transcription of target genes via an enhanced binding ability to the MYBCORE motif to mediate reactive oxygen species scavenging in response to salt and osmotic stresses.

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

2020 ◽  
Vol 21 (3) ◽  
pp. 975 ◽  
Author(s):  
Xiaojun Pu ◽  
Lixin Yang ◽  
Lina Liu ◽  
Xiumei Dong ◽  
Silin Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Physcomitrella Patens ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Terrestrial Environments ◽  
Gene Structures ◽  
Myb Genes ◽  
Myb Proteins ◽  
R2r3 Myb

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

scholarly journals Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

2020 ◽  
Author(s):  
Cuiyu Liu ◽  
Yujie Zhao ◽  
Xueqing Zhao ◽  
Jianmei Dong ◽  
Zhaohe Yuan
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nitrogen Deficiency ◽  
Punica Granatum ◽  
Salt Resistance ◽  
Specific Expression ◽  
Multiple Sequence ◽  
Root Cells ◽  
Expression Levels

Abstract Backgrounds: Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate.Results: In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3–/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42− , but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency.Conclusions: Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study establishes a theoretical foundation for the further functional characterization of CLC genes in pomegranate.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1452
Author(s):  
Hui Huang ◽  
Hui Wang ◽  
Yan Tong ◽  
Yuhua Wang
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Light Response ◽  
Vital Role ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Expression Levels

Dendrobium catenatum is a member of epiphytic orchids with extensive range of pharmacological properties and ornamental values. Superoxide dismutase (SOD), a key member of antioxidant system, plays a vital role in protecting plants against oxidative damage caused by various biotic and abiotic stresses. So far, little is known about the SOD gene family in D. catenatum. In this study, eight SOD genes, including four Cu/ZnSODs, three FeSODs and one MnSOD, were identified in D. catenatum genome. Phylogenetic analyses of SOD proteins in D. catenatum and several other species revealed that these SOD proteins can be assigned to three subfamilies based on their metal co-factors. Moreover, the similarities in conserved motifs and gene structures in the same subfamily corroborated their classification and inferred evolutionary relationships. There were many hormone and stress response elements in DcaSODs, of which light responsiveness elements was the largest group. All DcaSODs displayed tissue-specific expression patterns and exhibited abundant expression levels in flower and leaf. According to public RNA-seq data and qRT-PCR analysis showed that the almost DcaSODs, except for DcaFSD2, were highly expressed under cold and drought treatments. Under heat, light, and salt stresses, DcaCSD1, DcaCSD2, DcaCSD3 were always significantly up-regulated, which may play a vital role in coping with various stresses. The expression levels of DcaFSD1 and DcaFSD2 were promoted by high light, suggesting their important roles in light response. These findings provided valuable information for further research on DcaSODs in D. catenatum.

scholarly journals Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cuiyu Liu ◽  
Yujie Zhao ◽  
Xueqing Zhao ◽  
Jianmei Dong ◽  
Zhaohe Yuan
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nitrogen Deficiency ◽  
Punica Granatum ◽  
Salt Resistance ◽  
Specific Expression ◽  
Multiple Sequence ◽  
Root Cells ◽  
Expression Levels

Abstract Backgrounds Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate. Results In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3−/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42−, but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency. Conclusions Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.

scholarly journals Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yao Chen ◽  
Panpan Zhu ◽  
Shaoyuan Wu ◽  
Yan Lu ◽  
Jian Sun ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Raw Material ◽  
Functional Study ◽  
Ipomoea Trifida ◽  
Specific Expression ◽  
Adverse Environmental Condition ◽  
In The Wild

Abstract Background GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown. Results In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses. Conclusions Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

scholarly journals Memory CD4+ T-cell–mediated protection depends on secondary effectors that are distinct from and superior to primary effectors

2012 ◽  
Vol 109 (38) ◽  
pp. E2551-E2560 ◽  
Author(s):  
Tara M. Strutt ◽  
K. Kai McKinstry ◽  
Yi Kuang ◽  
Linda M. Bradley ◽  
Susan L. Swain
Keyword(s):  
T Cell ◽  
Influenza A Virus ◽  
Influenza A ◽  
Expression Patterns ◽  
Memory Cell ◽  
Specific Expression ◽  
Follicular Helper ◽  
Organ Specific ◽  
Follicular Helper T Cell ◽  
And Migration

Whether differences between naive cell-derived primary (1°) and memory cell-derived secondary (2°) CD4+ T-cell effectors contribute to protective recall responses is unclear. Here, we compare these effectors directly after influenza A virus infection. Both develop with similar kinetics, but 2° effectors accumulate in greater number in the infected lung and are the critical component of memory CD4+ T-cell–mediated protection against influenza A virus, independent of earlier-acting memory-cell helper functions. Phenotypic, functional, and transcriptome analyses indicate that 2° effectors share organ-specific expression patterns with 1° effectors but are more multifunctional, with more multicytokine (IFN-γ+/IL-2+/TNF+)-producing cells and contain follicular helper T-cell populations not only in the spleen and draining lymph nodes but also in the lung. In addition, they express more CD127 and NKG2A but less ICOS and Lag-3 than 1° effectors and express higher levels of several genes associated with survival and migration. Targeting two differentially expressed molecules, NKG2A and Lag-3, reveals differential regulation of 1° and 2° effector functions during pathogen challenge.

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