RNA-Seq Transcriptome Profiling Reveals Differentially Expressed Genes Involved in Sex Expression in Melon

Crop Science ◽  
2015 ◽  
Vol 55 (4) ◽  
pp. 1686-1695 ◽  
Author(s):  
Peng Gao ◽  
Yunyan Sheng ◽  
Feishi Luan ◽  
Hongyan Ma ◽  
Shi Liu
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Sex Expression ◽  
Differentially Expressed ◽  
Rna Seq

scholarly journals Transcriptome profiling provides new insights into florets number difference of inflorescence in lavandula angustifolia

2020 ◽  
Author(s):  
haiping hao ◽  
xiao pei zhu ◽  
Hui Li ◽  
Jian Gong ◽  
Amjad Farooq ◽  
...  
Keyword(s):  
Essential Oil ◽  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Extraction Methods ◽  
Essential Oil Composition ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Composition ◽  
Aba Metabolism ◽  
Aba Content

Abstract Background Lavender flowers essential oil had been for a variety of therapeutic and cosmetic purposes, and had been popular for centuries. The previous studies of lavender mainly focused on essential oil composition and extraction methods, ignoring the factors which affected the production of essential oils, such as the floret number. This study aims to get a deeper insight into florets number difference mechanism. Results Hormone profile showed positive correlation between ABA content and the number of florets while IAA was negatively correlated. RNA-Seq results showed that 2848 differentially expressed genes screened by comparing different florets samples in one plant. By analyzing dynamic changes of differentially expressed genes, many potentially interesting genes were identified that encoded putative regulators or key components of ABA metabolism and signaling transduction, such as NCED, PYL, PP2C, SnRK2. These genes were highlighted to reveal their importance in regulation of florets numbers. Conclusions 1. The different ABA concentrations lead to florets difference in the Lavandula angustifolia “JX-2” clusters; 2. ABA may affect the florets number by regulating IAA transport and accumulation. The results will be useful for a better understanding of the molecular mechanism on florets number difference that could be laid the foundation for molecular breeding of muti-flortes varieties.

Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach (Spinacia oleracea L.)

Genome ◽  
2021 ◽  
Author(s):  
Zhiyuan Liu ◽  
Haoying Wang ◽  
Zhaosheng Xu ◽  
Helong Zhang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Spinacia Oleracea ◽  
Transcriptome Profiling ◽  
Vital Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Spinacia Oleracea L

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA-sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2,278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.

scholarly journals Differentially Expressed Genes Associated with the Cabbage Yellow-Green-Leaf Mutant in the ygl-1 Mapping Interval with Recombination Suppression

2018 ◽  
Vol 19 (10) ◽  
pp. 2936 ◽  
Author(s):  
Xiaoping Liu ◽  
Hailong Yu ◽  
Fengqing Han ◽  
Zhiyuan Li ◽  
Zhiyuan Fang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Genomic Region ◽  
Differentially Expressed ◽  
Green Leaf ◽  
Rna Seq ◽  
Recombination Suppression ◽  
Leaf Mutant ◽  
Positional Mapping ◽  
Two Populations

Although the genetics and preliminary mapping of the cabbage yellow-green-leaf mutant YL-1 has been extensively studied, transcriptome profiling associated with the yellow-green-leaf mutant of YL-1 has not been discovered. Positional mapping with two populations showed that the yellow-green-leaf gene ygl-1 is located in a recombination-suppressed genomic region. Then, a bulk segregant RNA-seq (BSR) was applied to identify differentially expressed genes (DEGs) using an F3 population (YL-1 × 11-192) and a BC2 population (YL-1 × 01-20). Among the 37,286 unique genes, 5730 and 4118 DEGs were detected between the yellow-leaf and normal-leaf pools from the F3 and BC2 populations. BSR analysis with four pools greatly reduced the number of common DEGs from 4924 to 1112. In the ygl-1 gene mapping region with suppressed recombination, 43 common DEGs were identified. Five of the DEGs were related to chloroplasts, including the down-regulated Bo1g087310, Bo1g094360, and Bo1g098630 and the up-regulated Bo1g059170 and Bo1g098440. The Bo1g098440 and Bo1g098630 genes were excluded by qRT-PCR. Hence, we inferred that these three DEGs (Bo1g094360, Bo1g087310, and Bo1g059170) in the mapping interval may be tightly associated with the development of the yellow-green-leaf mutant phenotype.

scholarly journals Comparative RNA-Seq analysis reveals genes associated with masculinization in female Cannabis sativa

Planta ◽  
2021 ◽  
Vol 253 (1) ◽  
Author(s):  
Ayelign M. Adal ◽  
Ketan Doshi ◽  
Larry Holbrook ◽  
Soheil S. Mahmoud
Keyword(s):  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Patterns ◽  
Plant Biotechnology ◽  
Male Flower ◽  
Sex Expression ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Rna Profiling ◽  
Male Flowers

Abstract Main conclusion Using RNA profiling, we identified several silver thiosulfate-induced genes that potentially control the masculinization of female Cannabis sativa plants. Abstract Genetically female Cannabis sativa plants normally bear female flowers, but can develop male flowers in response to environmental and developmental cues. In an attempt to elucidate the molecular elements responsible for sex expression in C. sativa plants, we developed genetically female lines producing both female and chemically-induced male flowers. Furthermore, we carried out RNA-Seq assays aimed at identifying differentially expressed genes responsible for male flower development in female plants. The results revealed over 10,500 differentially expressed genes, of which around 200 potentially control masculinization of female cannabis plants. These genes include transcription factors and other genes involved in male organ (i.e., anther and pollen) development, as well as genes involved in phytohormone signalling and male-biased phenotypes. The expressions of 15 of these genes were further validated by qPCR assay confirming similar expression patterns to that of RNA-Seq data. These genes would be useful for understanding predisposed plants producing flowers of both sex types in the same plant, and help breeders to regulate the masculinization of female plants through targeted breeding and plant biotechnology.

scholarly journals HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 244 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Rossella Gratton ◽  
João Paulo Britto de Melo ◽  
José Leandro Andrade-Santos ◽  
Rafael Lima Guimarães ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Differentially Expressed Genes ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Infected Cells ◽  
Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

scholarly journals Phytophthora infestans Sporangia Produced in Culture and on Tomato Leaflet Lesions Show Marked Differences in Indirect Germination Rates, Aggressiveness, and Global Transcription Profiles

2019 ◽  
Vol 32 (5) ◽  
pp. 515-526 ◽  
Author(s):  
William E. Fry ◽  
Sean P. Patev ◽  
Kevin L. Myers ◽  
Kan Bao ◽  
Zhangjun Fei
Keyword(s):  
Phytophthora Infestans ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Moist Chamber ◽  
Field Isolates ◽  
Rxlr Effectors ◽  
Transcription Profiles ◽  
Independent Field ◽  
Pure Cultures

Sporangia of Phytophthora infestans from pure cultures on agar plates are typically used in lab studies, whereas sporangia from leaflet lesions drive natural infections and epidemics. Multiple assays were performed to determine if sporangia from these two sources are equivalent. Sporangia from plate cultures showed much lower rates of indirect germination and produced much less disease in field and moist-chamber tests. This difference in aggressiveness was observed whether the sporangia had been previously incubated at 4°C (to induce indirect germination) or at 21°C (to prevent indirect germination). Furthermore, lesions caused by sporangia from plates produced much less sporulation. RNA-Seq analysis revealed that thousands of the >17,000 P. infestans genes with a RPKM (reads per kilobase of exon model per million mapped reads) >1 were differentially expressed in sporangia obtained from plate cultures of two independent field isolates compared with sporangia of those isolates from leaflet lesions. Among the significant differentially expressed genes (DEGs), putative RxLR effectors were overrepresented, with almost half of the 355 effectors with RPKM >1 being up- or downregulated. DEGs of both isolates include nine flagellar-associated genes, and all were down-regulated in plate sporangia. Ten elicitin genes were also detected as DEGs in both isolates, and nine (including INF1) were up-regulated in plate sporangia. These results corroborate previous observations that sporangia produced from plates and leaflets sometimes yield different experimental results and suggest hypotheses for potential mechanisms. We caution that use of plate sporangia in assays may not always produce results reflective of natural infections and epidemics.

scholarly journals Bioinformatics-based Screening of Key Genes for Saponin Metabolism in Quinoa

2021 ◽  
Author(s):  
Chengang Guo ◽  
Zhimin wei ◽  
Wei Lyu ◽  
Yanlou Geng
Keyword(s):  
Differentially Expressed Genes ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Hierarchical Cluster ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Differential Analysis ◽  
Rna Seq ◽  
Protein Coding ◽  
Key Genes

Abstract Quinoa saponins have complex, diverse and evident physiologic activities. However, the key regulatory genes for quinoa saponin metabolism are not yet well studied. The purpose of this study was to explore genes closely related to quinoa saponin metabolism. In this study, the significantly differentially expressed genes in yellow quinoa were firstly screened based on RNA-seq technology. Then, the key genes for saponin metabolism were selected by gene set enrichment analysis (GSEA) and principal component analysis (PCA) statistical methods. Finally, the specificity of the key genes was verified by hierarchical clustering. The results of differential analysis showed that 1654 differentially expressed genes were achieved after pseudogenes deletion. Therein, there were 142 long non-coding genes and 1512 protein-coding genes. Based on GSEA analysis, 116 key candidate genes were found to be significantly correlated with quinoa saponin metabolism. Through PCA dimension reduction analysis, 57 key genes were finally obtained. Hierarchical cluster analysis further demonstrated that these key genes can clearly separate the four groups of samples. The present results could provide references for the breeding of sweet quinoa and would be helpful for the rational utilization of quinoa saponins.

scholarly journals Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria×ananassa)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4976 ◽  
Author(s):  
Panpan Hu ◽  
Gang Li ◽  
Xia Zhao ◽  
Fengli Zhao ◽  
Liangjie Li ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Fragaria Ananassa ◽  
Mads Box ◽  
Cell Wall Modification ◽  
Ripening Process ◽  
Fruit Development And Ripening

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of fiveubiquitin-conjugating enzymesand 10MADS-box transcription factorswere differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics inFragaria × ananassa.

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