scholarly journals De novo assembly of expressed transcripts and analysis of pistil to identify genes involved in early stage of pollination in Liriodendron chinense

2017 ◽  
Author(s):  
Ming Li ◽  
Kun Wang ◽  
Rebecca Njeri Damaris ◽  
Pingfang Yang
Keyword(s):  
Pollen Tube ◽  
Sexual Reproduction ◽  
Differentially Expressed Genes ◽  
De Novo ◽  
Early Stage ◽  
Average Length ◽  
Differentially Expressed ◽  
Seed Setting ◽  
Sequencing Data ◽  
Liriodendron Chinense

Plant sexual reproduction is a complicated and a key biological process with profuse interactions between pollen and pistil. This process determines whether fertilization will be successful or not and thus affect the seed setting. To explore the reason why L. chinense has a low seed setting ratio, transcriptome analysis on pistils of L. chinense during pollination were conducted. After analyzing the sequencing data, 206,858 unigenes with an average length of 646 bp were generated using the assembled transcripts. Among total unigenes, 3844 genes which expression fold change during early stage of pollination was higher or lower than 10 were selected as significant differentially expressed genes. 54 differentially expressed genes involved in sexual reproduction processes including the regulation of pollen tube growth process and double fertilization process might be partially causing the low seed setting in L. chinense. These results indicated that the barrier between pollen tube and pistil might be the reason why L. chinense have low seed setting. This study might be helpful to understand why L. chinense has such a low seed setting ratio.

scholarly journals De novo assembly of expressed transcripts and analysis of pistil to identify genes involved in early stage of pollination in Liriodendron chinense

2017 ◽  
Author(s):  
Ming Li ◽  
Kun Wang ◽  
Rebecca Njeri Damaris ◽  
Pingfang Yang
Keyword(s):  
Pollen Tube ◽  
Sexual Reproduction ◽  
Differentially Expressed Genes ◽  
De Novo ◽  
Early Stage ◽  
Average Length ◽  
Differentially Expressed ◽  
Seed Setting ◽  
Sequencing Data ◽  
Liriodendron Chinense

Plant sexual reproduction is a complicated and a key biological process with profuse interactions between pollen and pistil. This process determines whether fertilization will be successful or not and thus affect the seed setting. To explore the reason why L. chinense has a low seed setting ratio, transcriptome analysis on pistils of L. chinense during pollination were conducted. After analyzing the sequencing data, 206,858 unigenes with an average length of 646 bp were generated using the assembled transcripts. Among total unigenes, 3844 genes which expression fold change during early stage of pollination was higher or lower than 10 were selected as significant differentially expressed genes. 54 differentially expressed genes involved in sexual reproduction processes including the regulation of pollen tube growth process and double fertilization process might be partially causing the low seed setting in L. chinense. These results indicated that the barrier between pollen tube and pistil might be the reason why L. chinense have low seed setting. This study might be helpful to understand why L. chinense has such a low seed setting ratio.

scholarly journals Analysis of Differentially Expressed Genes of Chrysoperla sinica Related to Flight Capacity by Transcriptome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhong-Fang Liu ◽  
Yao-yao Liang ◽  
Xiao-ting Sun ◽  
Jing Yang ◽  
Peng-Jiu Zhang ◽  
...  
Keyword(s):  
Biological Control ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Insect Pests ◽  
Average Length ◽  
Differentially Expressed ◽  
Acid Decarboxylase ◽  
Flight Capacity ◽  
Different Ages

Abstract The lacewing Chrysoperla sinica (Tjeder) is a common natural enemy of many insect pests in China and is frequently employed for biological control programs. Adults make migratory flights after emergence, which reduces their effectiveness as biological control agents. Previously, we proved that 2-d-old unmated females exhibited significantly stronger flight ability than 3-d-old ones. Meanwhile, 3-d-old unmated adults flew significantly longer distances than mated ones. In this study, Illumina RNA sequencing was performed to characterize differentially expressed genes (DEGs) between virgin and mated adults of different ages in a single female strain of C. sinica. In total, 713,563,726 clean reads were obtained and de novo assembled into 109,165 unigenes with an average length of 847 bp (N50 of 1,754 bp), among which 4,382 (4.01%) unigenes matched known proteins. Based on these annotations, many putative transcripts were related to C. sinica’s flight capacity and muscle structure, energy supply, growth, development, environmental adaptability, and metabolism of nutritional components and bioactive components. In addition, the differential expression of transcripts between different ages and mating status were analyzed, and DEGs participating in flight capacity and muscles were detected, including glutathione hydrolase, NAD-specific glutamate dehydrogenase, aminopeptidase, and acidic amino acid decarboxylase. The DEGs with functions associated with flight capacity and muscles exhibited higher transcript levels for younger (2 d--old) virgins. This comprehensive C. sinica transcriptomic data provide a foundation for a better understanding of the molecular mechanisms underlying the flight capacity to meet the physiological demands of flight muscles in C. sinica.

scholarly journals Transcriptome analysis of Fenneropenaeus chinensis (Decapoda: Penaeidae) after low-salinity exposure identifies differentially expressed genes in pathways potentially related to osmoregulation

2020 ◽  
Author(s):  
Jun Liu ◽  
Lei Zhang ◽  
Zhengfei Wang ◽  
Daizhen Zhang ◽  
Shiguang Shao ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo ◽  
Average Length ◽  
Fenneropenaeus Chinensis ◽  
Differentially Expressed ◽  
Control Group ◽  
Molecular Response ◽  
Atpase Subunit ◽  
Low Salinity ◽  
Salinity Adaptations

AbstractAbility to tolerate low salinity is a key factor affecting the distribution of the Chinese shrimp (Fenneropenaeus chinensis). Although previous studies have investigated the mechanisms underlying adaptations to low salinity in some crustaceans, little is known about low-salinity adaptations in F. chinensis, particularly at the molecular level. Here, to identify genes potentially associated with the molecular response of F. chinensis to low-salinity exposure, we compared the transcriptomes of F. chinensis in low-salinity (5 ppt) and normal-salinity (20 ppt) environments. In total, 45,297,936 and 44,685,728 clean reads were acquired from the low-salinity and control groups, respectively. De novo assembly of the clean reads yielded 159,130 unigenes, with an average length of 662.82 bp. Of these unigenes, only a small fraction (10.5% on average) were successfully annotated against six databases. We identified 3,658 differentially expressed genes (DEGs) between the low-salinity group and the control group: 1,755 DEGs were downregulated in the low-salinity group as compared to the control, and 1,903 were upregulated. Of these DEGs, 282 were significantly overrepresented in 38 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Notably, several DEGs were associated with pathways important for osmoregulation, including the mineral absorption pathway (ATP1A, Sodium/potassium-transporting ATPase subunit alpha; CLCN2, Chloride channel 2; HMOX2, Heme oxygenase 2; SLC40A1/FPN1, Solute carrier family 40 iron-regulated transporter, member 1), the vasopressin-regulated water reabsorption pathway (AQP4, Aquaporin-4; VAMP2, Vesicle-associated membrane protein 2; RAB5, Ras-related protein Rab-5) and the ribosome pathway. Our results help to clarify the molecular basis of low-salinity adaptations in F. chinensis.

scholarly journals De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu-Fu Gao ◽  
Dong-Hui Zhao ◽  
Jia-Qi Zhang ◽  
Jia-Shuo Chen ◽  
Jia-Lin Li ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo ◽  
Regulatory Genes ◽  
Differentially Expressed ◽  
Anthocyanin Synthesis ◽  
Leaf Color ◽  
Metabolite Analysis ◽  
Color Formation ◽  
Content Change ◽  
Final Color

Abstract Background Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-leaf tree native to Northeastern China, however, there was less knowledge in Acer about anthocyanins biosynthesis and many steps of the pathway remain unknown to date. Results Anthocyanins metabolite and transcript profiling were conducted using HPLC and ESI-MS/MS system and high-throughput RNA sequencing respectively. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside and Cyanidin 3, 5-O-diglucoside were abundant, especially Cyanidin 3, 5-O-diglucoside displayed significant differences in content change at two periods, meaning it may be play an important role for the final color. Transcriptome identification showed that a total of 67.47 Gb of clean data were obtained from our sequencing results. Functional annotation of unigenes, including comparison with COG and GO databases, yielded 35,316 unigene annotations. 16,521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. The genes related to leaf color formation including PAL, ANS, DFR, F3H were selected. Also, we screened out the regulatory genes such as MYB, bHLH and WD40. Combined with the detection of metabolites, the gene pathways related to anthocyanin synthesis were analyzed. Conclusions Cyanidin 3, 5-O-diglucoside played an important role for the final color. The genes related to leaf color formation including PAL, ANS, DFR, F3H and regulatory genes such as MYB, bHLH and WD40 were selected. This study enriched the available transcriptome information for A. pseudosieboldianum and identified a series of differentially expressed genes related to leaf color, which provides valuable information for further study on the genetic mechanism of leaf color expression in A. pseudosieboldianum.

scholarly journals RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

2021 ◽  
Vol 8 ◽  
Author(s):  
Kirsten E. McLoughlin ◽  
Carolina N. Correia ◽  
John A. Browne ◽  
David A. Magee ◽  
Nicolas C. Nalpas ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Mycobacterium Bovis ◽  
Peripheral Blood ◽  
Post Infection ◽  
Time Course ◽  
De Novo ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Infection Time ◽  
Time Point

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

scholarly journals Bioinformatics analysis of differentially expressed genes and identification of an miRNA–mRNA network associated with entorhinal cortex and hippocampus in Alzheimer’s disease

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Haoming Li ◽  
Linqing Zou ◽  
Jinhong Shi ◽  
Xiao Han
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Differentially Expressed Genes ◽  
Entorhinal Cortex ◽  
Molecular Mechanisms ◽  
Kegg Pathway ◽  
Neurodegenerative Disorder ◽  
Early Stage ◽  
Differentially Expressed ◽  
Hub Genes

Abstract Background Alzheimer’s disease (AD) is a fatal neurodegenerative disorder, and the lesions originate in the entorhinal cortex (EC) and hippocampus (HIP) at the early stage of AD progression. Gaining insight into the molecular mechanisms underlying AD is critical for the diagnosis and treatment of this disorder. Recent discoveries have uncovered the essential roles of microRNAs (miRNAs) in aging and have identified the potential of miRNAs serving as biomarkers in AD diagnosis. Methods We sought to apply bioinformatics tools to investigate microarray profiles and characterize differentially expressed genes (DEGs) in both EC and HIP and identify specific candidate genes and pathways that might be implicated in AD for further analysis. Furthermore, we considered that DEGs might be dysregulated by miRNAs. Therefore, we investigated patients with AD and healthy controls by studying the gene profiling of their brain and blood samples to identify AD-related DEGs, differentially expressed miRNAs (DEmiRNAs), along with gene ontology (GO) analysis, KEGG pathway analysis, and construction of an AD-specific miRNA–mRNA interaction network. Results Our analysis identified 10 key hub genes in the EC and HIP of patients with AD, and these hub genes were focused on energy metabolism, suggesting that metabolic dyshomeostasis contributed to the progression of the early AD pathology. Moreover, after the construction of an miRNA–mRNA network, we identified 9 blood-related DEmiRNAs, which regulated 10 target genes in the KEGG pathway. Conclusions Our findings indicated these DEmiRNAs having the potential to act as diagnostic biomarkers at an early stage of AD.

scholarly journals Differentially Expressed Genes Extracted by the Tensor Robust Principal Component Analysis (TRPCA) Method

Complexity ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yue Hu ◽  
Jin-Xing Liu ◽  
Ying-Lian Gao ◽  
Sheng-Jun Li ◽  
Juan Wang
Keyword(s):  
Principal Component Analysis ◽  
Differentially Expressed Genes ◽  
Principal Component ◽  
Component Analysis ◽  
Differentially Expressed ◽  
Low Rank ◽  
Cancer Gene ◽  
Sequencing Data ◽  
Robust Principal Component Analysis ◽  
The Matrix

In the big data era, sequencing technology has produced a large number of biological sequencing data. Different views of the cancer genome data provide sufficient complementary information to explore genetic activity. The identification of differentially expressed genes from multiview cancer gene data is of great importance in cancer diagnosis and treatment. In this paper, we propose a novel method for identifying differentially expressed genes based on tensor robust principal component analysis (TRPCA), which extends the matrix method to the processing of multiway data. To identify differentially expressed genes, the plan is carried out as follows. First, multiview data containing cancer gene expression data from different sources are prepared. Second, the original tensor is decomposed into a sum of a low-rank tensor and a sparse tensor using TRPCA. Third, the differentially expressed genes are considered to be sparse perturbed signals and then identified based on the sparse tensor. Fourth, the differentially expressed genes are evaluated using Gene Ontology and Gene Cards tools. The validity of the TRPCA method was tested using two sets of multiview data. The experimental results showed that our method is superior to the representative methods in efficiency and accuracy aspects.

scholarly journals Transcriptome Analysis of ‘Haegeum’ Gold Kiwifruit Following Ethylene Treatment to Improve Postharvest Ripening Quality

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 487 ◽  
Author(s):  
Shimeles Tilahun ◽  
Han Ryul Choi ◽  
Hyok Kwon ◽  
Sung Min Park ◽  
Do Su Park ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Average Length ◽  
Titratable Acidity ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Sequencing Platform ◽  
Ethylene Treatment ◽  
Control Fruit

Fruit ripening involves changes in physical, physiological and metabolic activities through the actions of enzymes and regulatory genes. This study was initiated to identify the genes related to the ripening of kiwifruit. Gold ‘Haegeum’ kiwifruit is a yellow-fleshed kiwifruit cultivar usually used for fresh marketing. The fruit is harvested at a physiologically mature but unripe stage for proper storage, marketing distribution and longer shelf life. To identify the differentially expressed genes (DEGs) during ripening, fruit treated with ethylene were compared with control fruit that ripened naturally without ethylene treatment. Firmness, respiration rate, ethylene production rate, total soluble solids (TSS), titratable acidity (TA), brix acid ratio (BAR) and overall acceptability were taken during the study as fruit ripening indicators. Total mRNAs were sequenced by Illumina high-throughput sequencing platform and the transcriptome gene set was constructed by de novo assembly. We identified 99,601 unigenes with an average length of 511.77 bp in transcriptome contigs. A total of 28,582 differentially expressed unigenes were identified in the ethylene treatment vs. control. Of these 28,582 unigenes, 13,361 and 15,221 genes were up- and downregulated, respectively, in the treated fruit. The results also showed that 1682 and 855 genes were up- and downregulated, respectively, more than 2-fold at p < 0.05 in fruit treated with ethylene as compared with the control fruit. Moreover, we identified 75 genes showing significantly different expression; 42 were upregulated, and 33 were downregulated. A possible category of the identified ripening-related genes was also made. The findings of this study will add to the available information on the effect of ethylene treatment on ripening and the related changes of kiwifruit at the genomic level, and it could assist the further study of genes related to ripening for kiwifruit breeding and improvement.

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