scholarly journals Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data

2018 ◽  
Author(s):  
Shengcai Liu ◽  
Liyun Peng ◽  
Junfei Pan ◽  
Xiao Wang ◽  
Chunli Zhao ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Sequencing Data ◽  
Amaranthus Tricolor ◽  
Sequencing Platform ◽  
Transcriptome Database ◽  
Polymerase Chain ◽  
Illumina Sequencing Platform ◽  
Illumina Sequencing Data

Betalains are abundant in amaranth plants. Additionally, the betalain molecular structure and metabolic pathway differ from those of betanin in beet plants. To date, only a few studies have examined the regulatory roles of miRNAs in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 198 known and 41 novel miRNAs. Moreover, 216 miRNAs were distributed in 44 miRNA families, including miR156, miR159, miR160, miR166, miR172, miR319, miR167, miR396, and miR398. An analysis of all unigene sequences in an amaranth transcriptome database resulted in the detection of 493 target genes for the 239 screened miRNAs. The targets included SPL2, ARF18, ARF6, and NAC. A quantitative real-time polymerase chain reaction validation of 20 miRNAs and nine target genes revealed expression-level differences between the red and green sectors of amaranth leaves. This study involved the application of an Illumina sequencing platform to identify miRNAs regulating betalain metabolism in amaranth plants. The data presented herein may provide insights into the molecular mechanisms underlying the regulation of betalain biosynthesis in amaranth and other plant species.

scholarly journals Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data

2018 ◽  
Author(s):  
Shengcai Liu ◽  
Liyun Peng ◽  
Junfei Pan ◽  
Xiao Wang ◽  
Chunli Zhao ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Sequencing Data ◽  
Amaranthus Tricolor ◽  
Sequencing Platform ◽  
Transcriptome Database ◽  
Polymerase Chain ◽  
Illumina Sequencing Platform ◽  
Illumina Sequencing Data

Betalains are abundant in amaranth plants. Additionally, the betalain molecular structure and metabolic pathway differ from those of betanin in beet plants. To date, only a few studies have examined the regulatory roles of miRNAs in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 198 known and 41 novel miRNAs. Moreover, 216 miRNAs were distributed in 44 miRNA families, including miR156, miR159, miR160, miR166, miR172, miR319, miR167, miR396, and miR398. An analysis of all unigene sequences in an amaranth transcriptome database resulted in the detection of 493 target genes for the 239 screened miRNAs. The targets included SPL2, ARF18, ARF6, and NAC. A quantitative real-time polymerase chain reaction validation of 20 miRNAs and nine target genes revealed expression-level differences between the red and green sectors of amaranth leaves. This study involved the application of an Illumina sequencing platform to identify miRNAs regulating betalain metabolism in amaranth plants. The data presented herein may provide insights into the molecular mechanisms underlying the regulation of betalain biosynthesis in amaranth and other plant species.

scholarly journals Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Michael M. Karl ◽  
Anja Poehlein ◽  
Frank R. Bengelsdorf ◽  
Rolf Daniel ◽  
Peter Dürre
Keyword(s):  
Carbon Monoxide ◽  
Genome Sequence ◽  
Illumina Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequencing Data ◽  
Circular Chromosome ◽  
Content Type ◽  
Illumina Sequencing Data

ABSTRACT Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and cytochrome-containing autotrophic acetogen that is able to convert carbon monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (4.59 Mb).

scholarly journals QuicK-mer: A rapid paralog sensitive CNV detection pipeline

2015 ◽  
Author(s):  
Feichen Shen ◽  
Jeffrey Kidd
Keyword(s):  
High Throughput ◽  
Illumina Sequencing ◽  
Copy Number ◽  
Sequencing Data ◽  
Genome Copy ◽  
Genome Copy Number ◽  
Downstream Analysis ◽  
Cnv Detection ◽  
Illumina Sequencing Data ◽  
Control Regions

QuicK-mer is a unified pipeline for estimating genome copy-number from high-throughput Illumina sequencing data. QuicK-mer utilizes the Jellyfish application to efficiently tabulate counts of predefined sets of k-mers. The program performs GC-normalization using defined control regions and reports paralog-specific estimates of copy-number suitable for downstream analysis. The package is freely available at https://github.com/KiddLab/QuicK-mer

scholarly journals Using exosomal miRNAs extracted from follicular fluid to investigate their role in porcine oocyte development

2020 ◽  
Author(s):  
Junhe Hu ◽  
Jinyi Dong ◽  
Zhi Zeng ◽  
Juan Wu ◽  
Xiansheng Tan ◽  
...  
Keyword(s):  
Oocyte Maturation ◽  
Follicular Fluid ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Oocyte Development ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Genome Database ◽  
Exosomal Mirnas ◽  
Porcine Oocyte

Abstract Follicular development is crucial to normal oocyte maturation, with follicular size closely related to oocyte maturation. To better understand the molecular mechanisms behind porcine oocyte maturation, we obtained exosomal miRNA from porcine follicular fluid (PFF). These miRNA samples were then sequenced and analyzed regarding their different follicular sizes, as described in the methods section. First, these results showed that this process successfully isolated PFF exosomes. Nearly all valid reads from the PFF exosomal sequencing data were successfully mapped to the porcine genome database. Second, we used hierarchical clustering methods to determine that significantly expressed miRNAs were clustered into A, B, C, and D groups in our heatmap according to different follicle sizes. These results allowed for the targeting of potential mRNAs genes related to porcine oocyte development. Third, we chose ten, significantly expressed miRNAs and predicted their target genes for further GO analysis. These results showed that the expression levels of neurotransmitter secretion genes were greatly changed, as were many target genes involved in the regulation of FSH secretion. Notably, these are genes that are very closely related to oocyte maturation in growing follicles. We then used pathway analysis for these targeted genes based on the originally selected ten miRNAs. Results indicated that the pathways were mainly related to the biosynthesis of TGF-beta and its signaling pathway, which are very closely related to reproductive system functions. Finally, these exosomal miRNAs obtained from PFF may provide a valuable addition to our understanding of the mechanism of porcine oocyte maturation. It is also likely that these exosomal miRNAs could function as molecular biomarkers to choose high-quality oocytes and allow for in vitro porcine embryo production.

scholarly journals MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses

2021 ◽  
Vol 9 (1) ◽  
pp. 6
Author(s):  
Jingxian Zhang ◽  
Jiping Shi ◽  
Chenyang Yuan ◽  
Xiangcen Liu ◽  
Guilin Du ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Lipid Accumulation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Profile Analysis ◽  
Critical Role ◽  
Lipid Transport ◽  
Nitrogen Deprivation ◽  
Sequencing Platform ◽  
Novel Mirna

Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.

scholarly journals Using exosomal miRNAs extracted from porcine follicular fluid to investigate their role in oocyte development

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Junhe Hu ◽  
Jinyi Dong ◽  
Zhi Zeng ◽  
Juan Wu ◽  
Xiansheng Tan ◽  
...  
Keyword(s):  
Oocyte Maturation ◽  
Follicular Fluid ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Oocyte Development ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Genome Database ◽  
Exosomal Mirnas ◽  
Porcine Oocyte

Abstracts Background Follicular development is crucial to normal oocyte maturation, with follicular size closely related to oocyte maturation. To better understand the molecular mechanisms behind porcine oocyte maturation, we obtained exosomal miRNA from porcine follicular fluid (PFF). These miRNA samples were then sequenced and analyzed regarding their different follicular sizes, as described in the methods section. Results First, these results showed that this process successfully isolated PFF exosomes. Nearly all valid reads from the PFF exosomal sequencing data were successfully mapped to the porcine genome database. Second, we used hierarchical clustering methods to determine that significantly expressed miRNAs were clustered into A, B, C, and D groups in our heatmap according to different follicle sizes. These results allowed for the targeting of potential mRNAs genes related to porcine oocyte development. Third, we chose ten, significantly expressed miRNAs and predicted their target genes for further GO analysis. These results showed that the expression levels of neurotransmitter secretion genes were greatly changed, as were many target genes involved in the regulation of FSH secretion. Notably, these are genes that are very closely related to oocyte maturation in growing follicles. We then used pathway analysis for these targeted genes based on the originally selected ten miRNAs. Results indicated that the pathways were mainly related to the biosynthesis of TGF-beta and its signaling pathway, which are very closely related to reproductive system functions. Conclusions Finally, these exosomal miRNAs obtained from PFF may provide a valuable addition to our understanding of the mechanism of porcine oocyte maturation. It is also likely that these exosomal miRNAs could function as molecular biomarkers to choose high-quality oocytes and allow for in vitro porcine embryo production.

Sign in / Sign up

Export Citation Format

Share Document