scholarly journals High-throughput sequencing analysis identified microRNAs associated with egg production in ducks ovaries

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8440
Author(s):  
Mohan Qiu ◽  
Zengrong Zhang ◽  
Xia Xiong ◽  
Huarui Du ◽  
Qingyun Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Egg Production ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Egg Laying ◽  
Sequencing Analysis ◽  
Pathway Network ◽  
Qrt Pcr ◽  
Meat Type

Background MicroRNAs (miRNAs) exist widely and are involved in multiple biological processes in ducks, whereas the regulatory mechanism of miRNAs in egg laying of ducks has remained unclear. This study aims to reveal key miRNAs involved in the regulation of egg production in duck ovaries. Methods High-throughput sequencing was performed on four egg-type duck ovaries and four egg-meat-type duck ovaries at the start of the egg-laying stage. Quantitative reverse transcription PCR (qRT-PCR) validation was performed on differentially expressed miRNAs (DE miRNAs). Gene network of DEmiRNA-mRNA-pathway was constructed by Cytoscape. Results A total of 251 know miRNAs and 1,972 novel miRNAs were obtained from whole clean reads. Among the known miRNAs, we identified 21 DEmiRNAs, including eight down-regulated and 13 up-regulated miRNAs in egg-type ducks compared with egg-meat-type ducks. Among the novel miRNAs, we identified 70 DEmiRNAs, including 58 down-regulated and 12 up-regulated in egg-type ducks compared with egg-meat-type ducks. The expression patterns of four miRNAs were verified by qRT-PCR. The DEmiRNAs were involved in the function of response to folic acid and the pathway of valine, leucine and isoleucine degradation. Specific target genes of DEmiRNAs enrichment was found in some egg-laying regulation pathways, such as dopaminergic synapse, ovarian steroidogenesis and oocyte meiosis. The DEmiRNA-mRNA-pathway network including three DEmiRNAs, nine mRNAs and 11 pathways. apl-miR-194-5p and apl-miR-215-5p may be potential key miRNAs in regulating egg laying. Conclusions This study provided miRNAs profiles in ducks about egg laying and establish a theoretical basis for subsequent selection or modification of duck phenotypes at the molecular level.

scholarly journals High-throughput small RNA and transcriptome sequencing reveal reproduction-related microRNAs and mRNA in ovary of Geese in Counter-Season Production

2019 ◽  
Author(s):  
Jin-Shan Ran ◽  
Ling-Qian Yin ◽  
Jing-Jing Li ◽  
Yan-Qiang Tang ◽  
Jian Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Mirna Gene ◽  
Egg Laying ◽  
Differentially Expressed ◽  
Ovary Development ◽  
Regulation Mechanism ◽  
Pathway Network ◽  
Apoptosis Pathways

Abstract Background Broodiness is a phenomenon that occurs in most avian species and significantly reduces productivity. Several genes are known to play an important role in regulating the progress of reproduction, but the molecular regulation mechanism of broodiness remains unclear. In the current study, via high throughput sequencing, we identified and explored the differentially expressed miRNAs and mRNAs involved in ovarian atrophy. Results We identified a total of 901 mRNAs and 50 miRNAs that were differentially expressed in egg-laying and atrophic ovaries. Among them, numerous DEGs transcripts and target genes for miRNAs were significantly enriched in reproductive processes, cell proliferation, and apoptosis pathways. In addition, a miRNA- gene-pathway network was constructed by considering target relationships and correlation of the expression levels between ovary development-related genes and miRNAs. Conclusions We discovered mRNA and miRNAs transcripts that are candidate regulators of ovary development in broody geese. Our findings expanded our understanding of the functional of miRNAs in ovarian atrophy and demonstrated that RNA-Seq is a powerful tool for examining the molecular mechanism in regulating broodiness.

scholarly journals Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing

2019 ◽  
Vol 6 (1) ◽  
pp. 180735 ◽  
Author(s):  
Songtao Jiu ◽  
Xiangpeng Leng ◽  
Muhammad Salman Haider ◽  
Tianyu Dong ◽  
Le Guan ◽  
...  
Keyword(s):  
Plant Growth ◽  
High Throughput ◽  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Cu Stress ◽  
Gene Information

MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20–24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development and stress responses. With more copper (Cu) and copper containing compounds used as bactericides and fungicides in plants, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, two small RNA libraries were constructed from Cu-treated and water-treated (Control) leaves of ‘Summer Black’ grapevine. Following high-throughput sequencing and filtering, a total of 158 known and 98 putative novel miRNAs were identified in the two libraries. Among these, 100 known and 47 novel miRNAs were identified as differentially expressed under Cu stress. Subsequently, the expression patterns of nine Cu-responsive miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive miRNAs between high throughput sequencing and qRT-PCR assays. The targets prediction of miRNAs indicates that miRNA may regulate some transcription factors, including AP2, SBP, NAC, MYB and ARF during Cu stress. The target genes for two known and two novel miRNAs showed specific cleavage sites at the 10th and/or 11th nucleotide from the 5′-end of the miRNA corresponding to their miRNA complementary sequences. The findings will lay the foundation for exploring the role of the regulation of miRNAs in response to Cu stress and provide valuable gene information for breeding some Cu-tolerant grapevine cultivars.

scholarly journals The Effect of Different Pollination on the Expression of Dangshan Su Pear MicroRNA

2017 ◽  
Vol 2017 ◽  
pp. 1-18 ◽  
Author(s):  
Xi Cheng ◽  
Chongchong Yan ◽  
Jinyun Zhang ◽  
Chenhui Ma ◽  
Shumei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Quality ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cell Content ◽  
Qrt Pcr ◽  
Stone Cell ◽  
Negative Effect

The high-throughput sequencing of pear “Dangshan Su” × “Yali” (whose fruits lignin and stone cell content are high and quality is poor) and pear “Dangshan Su” × “Wonhwang” (whose fruits with low content of lignin and stone cell and the quality are better ) found that the expressions of these two miRNAs (pyr-1809 and pyr-novel-miR-144-3p) were significantly different; their corresponding target genes encode two kinds of laccase (Pbr018935.1 and Pbr003857.1). qRT-PCR results showed that these two enzymes are involved in the formation of lignin and stone cells and the existence of these two miRNAs has a negative effect on them. It was concluded that the effect of pollination on the development of stone cells may affect the synthesis of lignin, through the regulation of laccase controlled by miRNAs, and ultimately affect the formation of stone cell and fruit quality.

scholarly journals Effects of keratinocyte-derived and fibroblast-derived exosomes on human epidermal melanocytes

2021 ◽  
Vol 0 ◽  
pp. 1-10
Author(s):  
Hai-Xia Shi ◽  
Ru-Zhi Zhang ◽  
Li Xiao ◽  
Li Wang
Keyword(s):  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Tyrosinase Activity ◽  
The Other ◽  
Differentially Expressed ◽  
Ras Signaling ◽  
Sequencing Analysis ◽  
Melanin Synthesis

Background: Exosomes have been demonstrated to carry proteins, membrane lipids, mRNAs and microRNAs which can be transferred to surrounding cells and regulate the functions of those recipient cells. Objectives: The objective of the study was to investigate the effects of exosomes released by keratinocytes and fibroblasts on the proliferation, tyrosinase activity and melanogenesis of melanocytes. Methods: Melanocytes, keratinocytes and fibroblasts obtained from human foreskin were cultured and exosomes secreted by keratinocytes and fibroblasts were harvested from the culture supernatants by ultracentrifugation. Each exosome fraction was divided into two parts; one part was subjected to high-throughput sequencing using an Illumina HiSeq sequencer to characterize the microRNA expression profiles, while the other part was labeled with the fluorescent dye PKH67 and was then co-cultivated with epidermal melanocytes. Results: High-throughput sequencing analysis showed 168 differentially expressed microRNA within exosomes derived from keratinocytes and from fibroblasts, 97 of those being up-regulated with the other 71 down-regulated. Gene ontology analysis showed that the target genes responsible for these differentially expressed microRNAs were mainly enriched in the protein-binding region of molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that target genes regulated by differentially expressed microRNA were mainly involved in mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, cAMP signaling pathway and Wnt signaling pathway. Keratinocyte-derived exosomes were taken up by melanocytes co-cultured with them and promoted the proliferation, tyrosinase activity and melanin synthesis of those melanocytes. However, fibroblast-derived exosomes had no similar effects on melanocytes. Conclusion: Keratinocyte-derived exosomes but not fibroblast-derived exosomes were taken up by melanocytes in co-culture and significantly stimulated their proliferation, tyrosinase activity and melanin synthesis. Those different effects may be mainly due to the differential expression of microRNAs in exosomes derived from the different types of cells. Limitations: Electron microscopy of the obtained exosomes and in-depth study of apparently differentially expressed microRNAs were not performed.

scholarly journals Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (Benincasa hispida) Based on High-Throughput Sequencing

2021 ◽  
Vol 11 (21) ◽  
pp. 10068
Author(s):  
Jinqiang Yan ◽  
Min Wang ◽  
Wenrui Liu ◽  
Dasen Xie ◽  
Xiaoming He ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Specific Expression ◽  
Nac Transcription Factors ◽  
Benincasa Hispida ◽  
Wax Gourd

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20-24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.

scholarly journals High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 27 ◽  
Author(s):  
Marta Maciejewska ◽  
Magdalena Całusińska ◽  
Luc Cornet ◽  
Delphine Adam ◽  
Igor Pessi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Spatial Diversity ◽  
Sequencing Analysis
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