scholarly journals Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

2020 ◽  
Vol 21 (3) ◽  
pp. 1080
Author(s):  
Jawahar Lal Katara ◽  
Ram Lakhan Verma ◽  
Madhuchhanda Parida ◽  
Umakanta Ngangkham ◽  
Kutubuddin Ali Molla ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Carbon Fixation ◽  
Reference Genome ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Grain Filling ◽  
Rna Seq ◽  
Kegg Pathway Analysis ◽  
Expression Of Genes ◽  
Differential Expression Of Genes

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

scholarly journals Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 360
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Xue Li ◽  
Chenhe Wang
Keyword(s):  
Gene Expression ◽  
Olive Oil ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Minor Components ◽  
Harvest Time ◽  
Rna Seq ◽  
Optimal Harvest ◽  
Harvest Strategy ◽  
Different Color

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.

scholarly journals Differential Expression of Genes Related to the Formation of Giant Leaves in Triploid Poplar

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 920 ◽  
Author(s):  
Kang Du ◽  
Qiang Han ◽  
Ying Zhang ◽  
Xiangyang Kang
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Leaf Growth ◽  
Growth Hormones ◽  
Endogenous Hormones ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Expression Of Genes ◽  
Genes Expression ◽  
Differential Expression Of Genes

Plant polyploids tend to have large leaves, but their formation mechanism has not yet been well explained. Therefore, daily transcriptomic differences between triploids and diploids from a synthetic Populus sect. Tacamahaca three times a day (i.e., 04:00, 09:00, and 21:00) were investigated using high-throughput RNA-seq analysis. In this study, we identified several transcription factors associated with giant leaves. The combined effects included the high expression of several transcription factors (WRKY, MYB, etc.) and hormone-related genes (e.g., activates auxin, cytokine, and brassinosteroid synthesis-related genes) that accelerate the synthesis and accumulation of endogenous hormones. High levels of growth hormones were maintained by reducing the genes’ expression of hormone metabolism and degradation. The coordination of hormones accumulated sufficient materials and energy for leaf growth and development. Thereby, cell division and growth were accelerated which enhanced the photosynthesis of leaves, and the increased accumulation of photosynthetic products led to giant triploid leaves. This study lays the foundation for revealing the molecular mechanisms in the formation of giant leaves in polyploids.

scholarly journals Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data

2021 ◽  
Vol 8 ◽  
Author(s):  
Liliana Florea ◽  
Lindsay Payer ◽  
Corina Antonescu ◽  
Guangyu Yang ◽  
Kathleen Burns
Keyword(s):  
Frontal Cortex ◽  
Large Scale ◽  
Reference Genome ◽  
Expression Patterns ◽  
Data Sets ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Specific Expression ◽  
Human Frontal Cortex ◽  
Alternatively Spliced

Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns.

scholarly journals Subgenome Bias and Temporal Postponement of Gene Expression Contributes to the Distinctions of Fiber Quality in Gossypium Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Mei ◽  
Bowen Qi ◽  
Zegang Han ◽  
Ting Zhao ◽  
Menglan Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Rna Seq ◽  
Hub Genes ◽  
Hub Gene ◽  
Expression Of Genes ◽  
Multiple Dimensions ◽  
Cotton Species ◽  
Expression Bias

As two cultivated widely allotetraploid cotton species, although Gossypium hirsutum and Gossypium barbadense evolved from the same ancestor, they differ in fiber quality; the molecular mechanism of that difference should be deeply studied. Here, we performed RNA-seq of fiber samples from four G. hirsutum and three G. barbadense cultivars to compare their gene expression patterns on multiple dimensions. We found that 15.90–37.96% of differentially expressed genes showed biased expression toward the A or D subgenome. In particular, interspecific biased expression was exhibited by a total of 330 and 486 gene pairs at 10 days post-anthesis (DPA) and 20 DPA, respectively. Moreover, 6791 genes demonstrated temporal differences in expression, including 346 genes predominantly expressed at 10 DPA in G. hirsutum (TM-1) but postponed to 20 DPA in G. barbadense (Hai7124), and 367 genes predominantly expressed at 20 DPA in TM-1 but postponed to 25 DPA in Hai7124. These postponed genes mainly participated in carbohydrate metabolism, lipid metabolism, plant hormone signal transduction, and starch and sucrose metabolism. In addition, most of the co-expression network and hub genes involved in fiber development showed asymmetric expression between TM-1 and Hai7124, like three hub genes detected at 10 DPA in TM-1 but not until 25 DPA in Hai7124. Our study provides new insights into interspecific expression bias and postponed expression of genes associated with fiber quality, which are mainly tied to asymmetric hub gene network. This work will facilitate further research aimed at understanding the mechanisms underlying cotton fiber improvement.

scholarly journals Transcriptome profiling and comparison of Rhinanthus major and Rhinanthus minor reciprocal F1 hybrids during seed stratification and germination

2021 ◽  
Author(s):  
Khaled Mirzaei ◽  
Renate A. Wesselingh
Keyword(s):  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
F1 Hybrids ◽  
Rna Seq ◽  
Seed Formation ◽  
Maternal Parent ◽  
Expression Of Genes ◽  
Fitness Consequences ◽  
Hybrid Seeds ◽  
Rhinanthus Minor

Germination is a vital stage in a plants life cycle, and a different germination behavior of offspring in comparison to their parents can have fitness consequences. In studies on hybridization between Rhinanthus minor and R. major, low germination rates of F1 hybrids with R. major as the maternal parent have often been reported. In contrast, the F1m hybrid, with R. minor as the maternal parent, germinates readily and rapidly. In order to find the cause of this difference, we used RNA-Seq to obtain transcriptome profiles of F1a and F1m seeds during stratification at 4C and just after germination, after 40 days of stratification for the F1m seeds and 60 days for the F1a seeds. A comparison of the transcriptome of F1a seeds that had just germinated (60 days) with non-germinated F1a seeds after 40 and 60 days revealed 2918 and 1349 differentially expressed (DE) genes, respectively. For F1m seeds, 958 genes showed differential expression in germinated and non-germinated seeds after 40 days. The DE genes of F1a and F1m hybrids clustered into two separate groups, even though they had the same parents, and no differentially expression was found for plastid genes. Non-germinated F1a seeds had an abundance of enzymes and proteins associated with peroxidase activity, peroxiredoxin activity and nutrient reservoir activity. Expression of genes related to seed germination and seed development increased in non-germinated F1a hybrid seeds between 40 and 60 days of cold stratification. F1a seeds that had germinated showed an upregulation of genes related to the gibberellic acid-mediated signaling pathway and response to gibberellin, along with a low expression of DELLA superfamily. Although the results demonstrated strong differences in gene expression during stratification between the reciprocal hybrids, we could not identify its cause, since no plastid genes were differentially expressed. It is possible that differences in embryo development after seed formation and before stratification play a role, including epigenetic imprinting.

scholarly journals HMGR overexpression and interference affects the expression of steroidogenic genes and cholesterol content in bovine intramuscular adipocytes

2019 ◽  
Author(s):  
Xiaomu Liu ◽  
Wei You ◽  
Xianglun Zhang ◽  
Qing Jin ◽  
Xiuwen Tan ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Mevalonic Acid ◽  
Cholesterol Content ◽  
Rna Seq ◽  
Theoretical Understanding ◽  
Bovine Adipocytes ◽  
Steroidogenic Genes

Abstract Background:Previously, we found that mevalonic acid stimulates HMGR expression in bovine intramuscular adipocytes, and influences adipocyte differentiation. However, it remains unclear whether there is any direct link between HMGR, steroidogenic genes, and cholesterol content. RNA-Seq was conducted to determine the differences between the gene expression profiles of bovine adipocytes containing different HMGR expression constructs. Results:In total, 10 234 differentially expressed genes (DEGs) were found. Of these, 35 and 6 DEGs between the control and the overexpression groups were functionally related to lipid and energy metabolisms, respectively. Additionally, 43 and 8 DEGs between the control and the HMGR inhibition groups were related to lipid and energy metabolism. Additionally, several DEGs related to lipid and energy metabolism were identified between the HMGR overexpression group and the HMGR interference group. Several DEGs correlated positively or negatively with overexpression or inhibition of HMGR. We also found that, following activation or inhibition of the HMGR gene, AMPK and SIRT1 had opposite expression patterns in bovine intramuscular adipocytes. Interestingly, the HMGR gene was downregulated when HMGR was overexpressed, and upregulated when HMGR was inhibited. Conclusion:Our findings establish a theoretical understanding of signaling pathways involved in cholesterol synthesis by elucidating the relationships between key genes.

scholarly journals Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balázs Kalapos ◽  
Csilla Juhász ◽  
Eszter Balogh ◽  
Gábor Kocsy ◽  
István Tóbiás ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Carbon Fixation ◽  
Systemic Infection ◽  
Transcriptome Profiling ◽  
Hypersensitive Reaction ◽  
Post Inoculation ◽  
Rna Seq ◽  
Virus Infections ◽  
Transcriptional Reprogramming ◽  
Pepper Leaves

AbstractUpon virus infections, the rapid and comprehensive transcriptional reprogramming in host plant cells is critical to ward off virus attack. To uncover genes and defense pathways that are associated with virus resistance, we carried out the transcriptome-wide Illumina RNA-Seq analysis of pepper leaves harboring the L3 resistance gene at 4, 8, 24 and 48 h post-inoculation (hpi) with two tobamoviruses. Obuda pepper virus (ObPV) inoculation led to hypersensitive reaction (incompatible interaction), while Pepper mild mottle virus (PMMoV) inoculation resulted in a systemic infection without visible symptoms (compatible interaction). ObPV induced robust changes in the pepper transcriptome, whereas PMMoV showed much weaker effects. ObPV markedly suppressed genes related to photosynthesis, carbon fixation and photorespiration. On the other hand, genes associated with energy producing pathways, immune receptors, signaling cascades, transcription factors, pathogenesis-related proteins, enzymes of terpenoid biosynthesis and ethylene metabolism as well as glutathione S-transferases were markedly activated by ObPV. Genes related to photosynthesis and carbon fixation were slightly suppressed also by PMMoV. However, PMMoV did not influence significantly the disease signaling and defense pathways. RNA-Seq results were validated by real-time qPCR for ten pepper genes. Our findings provide a deeper insight into defense mechanisms underlying tobamovirus resistance in pepper.

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