scholarly journals Genome-Wide Analysis and Identification of the Aux/IAA Gene Family in Peach

2019 ◽  
Vol 20 (19) ◽  
pp. 4703 ◽  
Author(s):  
Dan Guan ◽  
Xiao Hu ◽  
Donghui Diao ◽  
Fang Wang ◽  
Yueping Liu
Keyword(s):  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Fruit Maturation ◽  
Auxin Response ◽  
Genome Wide ◽  
Potential Development ◽  
Fold Induction ◽  
Indole 3 Acetic Acid ◽  
Insight Into ◽  
Stony Hard

The Auxin/indole-3-acetic acid (Aux/IAA) repressor genes down-regulate the auxin response pathway during many stages of plant and fruit development. In order to determine if and how Aux/IAAs participate in governing texture and hardness in stone fruit maturation, we identified 23 Aux/IAA genes in peach, confirmed by the presence of four conserved domains. In this work, we used fluorescence microscopy with PpIAA-GFP fusion reporters to observe their nuclear localization. We then conducted PCR-based differential expression analysis in “melting” and “stony hard” varieties of peach, and found that in the “melting” variety, nine PpIAAs exhibited peak expression in the S4-3 stage of fruit maturation, with PpIAA33 showing the highest (>120-fold) induction. The expression of six PpIAAs peaked in the S4-2 stage, with PpIAA14 expressed the most highly. Only PpIAA15/16 showed higher expression in the “stony hard” variety than in the “melting” variety, both peaking in the S3 stage. In contrast, PpIAA32 had the highest relative expression in buds, flowers, young and mature leaves, and roots. Our study provides insights into the expression patterns of Aux/IAA developmental regulators in response to auxin during fruit maturation, thus providing insight into their potential development as useful markers for quantitative traits associated with fruit phenotype.

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals A role for microRNAs in the epigenetic control of sexually dimorphic gene expression in the human placenta

Epigenomics ◽  
2020 ◽  
Vol 12 (17) ◽  
pp. 1543-1558 ◽  
Author(s):  
Lauren A Eaves ◽  
Preeyaphan Phookphan ◽  
Julia E Rager ◽  
Jacqueline Bangma ◽  
Hudson P Santos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression Analysis ◽  
Sexually Dimorphic ◽  
Potential Mechanism ◽  
Master Regulators ◽  
Genome Wide ◽  
Sexually Dimorphic Expression ◽  
Insight Into ◽  
Dimorphic Gene Expression ◽  
Dimorphic Expression

Aim: The contribution of miRNAs as epigenetic regulators of sexually dimorphic gene expression in the placenta is unknown. Materials & methods: 382 placentas from the extremely low gestational age newborns (ELGAN) cohort were evaluated for expression levels of 37,268 mRNAs and 2,102 miRNAs using genome-wide RNA-sequencing. Differential expression analysis was used to identify differences in the expression based on the sex of the fetus. Results: Sexually dimorphic expression was observed for 128 mRNAs and 59 miRNAs. A set of 25 miRNA master regulators was identified that likely contribute to the sexual dimorphic mRNA expression. Conclusion: These data highlight sex-dependent miRNA and mRNA patterning in the placenta and provide insight into a potential mechanism for observed sex differences in outcomes.

scholarly journals Genome-Wide Analysis of Carboxylesterases (COEs) in the Whitefly, Bemisia tabaci (Gennadius)

2019 ◽  
Vol 20 (20) ◽  
pp. 4973
Author(s):  
Jixing Xia ◽  
Haifeng Xu ◽  
Zezhong Yang ◽  
Huipeng Pan ◽  
Xin Yang ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Expression Patterns ◽  
Invasive Pest ◽  
Neighbor Joining ◽  
Functional Categories ◽  
Genome Database ◽  
Genome Wide ◽  
A Genome ◽  
Multifunctional Enzymes ◽  
Insight Into

The whitefly (Bemisia tabaci), an important invasive pest that causes severe damage to crops worldwide, has developed resistance to a variety of insecticides. Carboxylesterases (COEs) are important multifunctional enzymes involved in the growth, development, and xenobiotic metabolism of insects. However, systematic studies on the COEs of B. tabaci are scarce. Here, 42 putative COEs in different functional categories were identified in the Mediterranean species of B. tabaci (B. tabaci MED) based on a genome database and neighbor-joining phylogeny. The expression patterns of the COEs were affected by the development of B. tabaci. The expression levels of six COEs were positively correlated with the concentration of imidacloprid to which B. tabaci adults were exposed. The mortality of B. tabaci MED adults fed dsBTbe5 (67.5%) and dsBTjhe2 (58.4%) was significantly higher than the adults fed dsEGFP (41.1%) when treated with imidacloprid. Our results provide a basis for functional research on COEs in B. tabaci and provide new insight into the imidacloprid resistance of B. tabaci.

scholarly journals Genome-wide Identification and Expression Pattern Analysis of BRI1-EMS–suppressor Transcription Factors in Tomato under Abiotic Stresses

2018 ◽  
Vol 143 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Yingmei Gao ◽  
Jingkang Hu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Functional Identification ◽  
Tomato Plants ◽  
Protein Motifs ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Regulated Gene Expression ◽  
Insight Into

BRI1-EMS-suppressor 1 (BES1) is a transcription factor (TF) that functions as a master regulator of brassinosteroid (BR)-regulated gene expression. Here, we provide a complete overview of Solanum lycopersicum BES1 (SLB) genes, including phylogeny, gene structure, protein motifs, chromosome locations and expression characteristics. Through bioinformatic analysis, we compared the sequences of SLB genes, arabidopsis (Arabidopsis thaliana) genes, and chinese cabbage (Brassica pekinensis) genes. All of the gene sequences were divided into three groups by cluster analysis. SLB genes were mapped to the eight tomato (S. lycopersicum) chromosomes. Bioinformatic analysis showed that SLB genes shares similarities with the proteins from other plants, though different species exhibit specific features. The expression patterns of SLB genes in various tissues and under different abiotic conditions were analyzed by quantitative reverse transcription polymerase chain reaction. SLB genes were found to be induced by multiple stresses, particularly salt stress, indicating that SLB genes may have important roles in the response to unfavorable environmental changes. This study provides insight into the evolution of SLB genes and may aid in the further functional identification of BES1 proteins and the response of tomato plants to different stresses.

scholarly journals Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinzi Yu ◽  
Zhaolan Mo ◽  
Xianghai Tang ◽  
Tian Gao ◽  
Yunxiang Mao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dehydration Stress ◽  
Pyropia Yezoensis ◽  
Genome Wide ◽  
Regulated Expression ◽  
Relative Conservation ◽  
Shock Proteins ◽  
Insight Into

Abstract Background Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis. Results We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution. Conclusions These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.

scholarly journals Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6677 ◽  
Author(s):  
Yanqing Zhang ◽  
Zaohai Zeng ◽  
Chengjie Chen ◽  
Caiqin Li ◽  
Rui Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Expression Patterns ◽  
Flower Formation ◽  
Auxin Response ◽  
Dimerization Domain ◽  
Litchi Chinensis ◽  
Regulatory Pathways ◽  
Fruit Abscission ◽  
Genome Wide ◽  
A Genome

Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.

scholarly journals Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruit of melting flesh and stony hard peach varieties

2019 ◽  
Author(s):  
Bin Tan ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
Wenfang Zeng ◽  
Xianbo Zheng ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Ubiquitin Ligase ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Stony Hard

Abstract Background Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3s family is still yet to be identified, and the functions of E3 ligase genes on fruit flesh are unknown in peach. Results In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four new types of proteins in the BTB subfamily were first identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM >1) in either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions The results of this study provide useful information for further understanding the functional characterization of the ubiquitin ligase genes in peach. In addition, the findings also provide the first clues of E3 ligase gene function in the regulation of peach ripening.

scholarly journals Genome-wide DNA methylation and gene expression patterns provide insight into polycystic ovary syndrome development

Oncotarget ◽  
2014 ◽  
Vol 5 (16) ◽  
pp. 6603-6610 ◽  
Author(s):  
Xiu-Xia Wang ◽  
Jing-Zan Wei ◽  
Jiao Jiao ◽  
Shu-Yi Jiang ◽  
Da-Hai Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Polycystic Ovary Syndrome ◽  
Polycystic Ovary ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Ovary Syndrome ◽  
Genome Wide ◽  
Insight Into

scholarly journals Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Bin Tan ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
Wenfang Zeng ◽  
Xianbo Zheng ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Ubiquitin Ligase ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Expression Patterns ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Stony Hard

Abstract Background Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach. Results In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

scholarly journals Genome-Wide Investigation of the Auxin Response Factor Gene Family in Tartary Buckwheat (Fagopyrum tataricum)

2018 ◽  
Vol 19 (11) ◽  
pp. 3526 ◽  
Author(s):  
Moyang Liu ◽  
Zhaotang Ma ◽  
Anhu Wang ◽  
Tianrun Zheng ◽  
Li Huang ◽  
...  
Keyword(s):  
Fruit Development ◽  
Expression Patterns ◽  
Auxin Response Factor ◽  
Tartary Buckwheat ◽  
Structure Evolution ◽  
Response Factor ◽  
Auxin Response ◽  
Fagopyrum Tataricum ◽  
Genome Wide ◽  
A Genome

Auxin signaling plays an important role in plant growth and development. It responds to various developmental and environmental events, such as embryogenesis, organogenesis, shoot elongation, tropical growth, lateral root formation, flower and fruit development, tissue and organ architecture, and vascular differentiation. However, there has been little research on the Auxin Response Factor (ARF) genes of tartary buckwheat (Fagopyrum tataricum), an important edible and medicinal crop. The recent publication of the whole-genome sequence of tartary buckwheat enables us to study the tissue and expression profile of the FtARF gene on a genome-wide basis. In this study, 20 ARF (FtARF) genes were identified and renamed according to the chromosomal distribution of the FtARF genes. The results showed that the FtARF genes belonged to the related sister pair, and the chromosomal map showed that the duplication of FtARFs was related to the duplication of the chromosome blocks. The duplication of some FtARF genes shows conserved intron/exon structure, which is different from other genes, suggesting that the function of these genes may be diverse. Real-time quantitative PCR analysis exhibited distinct expression patterns of FtARF genes in various tissues and in response to exogenous auxin during fruit development. In this study, 20 FtARF genes were identified, and the structure, evolution, and expression patterns of the proteins were studied. This systematic analysis laid a foundation for the further study of the functional characteristics of the ARF genes and for the improvement of tartary buckwheat crops.

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