scholarly journals Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zilong Zhao ◽  
Dan Liu ◽  
Yanjiao Cui ◽  
Suying Li ◽  
Dan Liang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Foxtail Millet ◽  
Differentially Expressed ◽  
High Yield ◽  
Yield Formation ◽  
Identification And Characterization

Abstract Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding.

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results Total RNA from milk exosomes was collected from healthy cows (n = 3, the control group) and S. aureus infected cows (n = 6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. The expression of two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (> 3.5) was significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

scholarly journals Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 591 ◽  
Author(s):  
Chen ◽  
Huo ◽  
Yang ◽  
Jian ◽  
Qu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Differentially Expressed ◽  
Oilseed Crop ◽  
Flower Bud ◽  
Mirna Profiling ◽  
Differentially Expressed Mirnas ◽  
Yield Formation ◽  
Architecture Component

Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.

Identification and characterization of microRNAs in white and black coated yak

2018 ◽  
Author(s):  
Wang-Dui Basang ◽  
Tian-Wu An ◽  
Xiao-Lin Luo ◽  
Yan-Bin Zhu ◽  
Luo-Bu Danjiu Danjiu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Coat Color ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Black And White ◽  
Kegg Pathways ◽  
Differentially Expressed Mirnas ◽  
Paired End Sequencing ◽  
Identification And Characterization

In this study, we used high-throughput technology to provide the first transcriptome dataset for differentially expressed miRNA in mixed pools of dermis tissue from black- and white-coated yak to research the possible molecular mechanisms of yak coat pigmentation. In this study, 92,636,002 and 95,917,842 clear reads were generated through Illumina paired-end sequencing. A total of 78 differentially expressed miRNAs (DEMs) were identified, including 59 upregulated and 19 downregulated miRNAs in the mixed pools of white-coated yak compared with the mixed pools of black-coated yak. In addition, 3634 genes were predicted as putative targets of DEMs. These DEGs related to 59 GO categories and were enriched in 216 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including melanogenesis and the Wnt signaling pathway. The results of the current study indicated that the coat color of the yak involved the transcriptional regulation process of miRNAs. These results provide helpful data to understand the molecular mechanisms of yak coat pigmentation.

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

2019 ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results: Total RNA from milk exosomes was collected from healthy cows (n=3, the control group) and S. aureus infected cows (n=6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log 2 fold changes (>3.5) were significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion: DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

scholarly journals Identification and Characterization of Long Non-Coding RNA in Tomato Roots under Salt Stress

2021 ◽  
Author(s):  
Ning Li ◽  
Zhongyu Wang ◽  
Baike Wang ◽  
Juan Wang ◽  
Ruiqiang Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Vegetable Crops ◽  
Tomato Roots ◽  
Non Coding Rnas

As one of the most important vegetable crops in the world, the production of tomatoes was restricted by salt stress. Therefore, it is of great interest to analyze the salt stress tolerance genes. As the non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides, long non-coding RNAs (lncRNAs) lack the ability of protein-coding, but they can play crucial roles in plant development and response to abiotic stresses by regulating gene expression. Nevertheless, there are few studies on the roles of salt-induced lncRNAs in tomatoes. Therefore, we selected wild tomato Solanum pennellii (S. pennellii) and cultivated tomato M82 to be materials. By high-throughput sequencing, 1044 putative lncRNAs were identified here. Among them, 154 and 137 lncRNAs were differentially expressed in M82 and S. pennellii, respectively. Through functional analysis of target genes of differentially expressed lncRNAs (DE-lncRNAs), some genes were found to respond positively to salt stress by participating in Abscisic Acid (ABA) signaling pathway, brassinosteroid (BR) signaling pathway, ethylene (ETH) signaling pathway and anti-oxidation process. We also construct a salt-induced lncRNA-mRNA co-expression network to dissect the putative mechanisms of high salt tolerance in S. pennellii. We analyze the function of salt-induced lncRNAs in tomato roots at the genome-wide levels for the first time. These results will contribute to understanding the molecular mechanisms of salt tolerance in tomatoes from the perspective of lncRNAs.

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

2019 ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results: Total RNA from milk exosomes was collected from healthy cows (n=3, the control group) and S. aureus infected cows (n=6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log 2 fold changes (>3.5) were significantly higher in mastitic milk infected with S. aureus. One target gene (V AT1L) of bta-miR-378 and five target genes (DYRK1B , MLLT3 , HP1BP3 , NPR2 and PGM1) of bta-miR-185 were validated. Conclusion: DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

Identification and Characterization of Heat-Responsive miRNAs and their Regulatory Network in Maize

2020 ◽  
Author(s):  
Yang Zhao ◽  
Qiye Wei ◽  
Tianci Chen ◽  
Lijuan Xu ◽  
Jing Liu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Regulatory Network ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Heat Stress Response ◽  
Yield And Quality ◽  
And Control ◽  
Identification And Characterization

Abstract Background: MicroRNAs (miRNAs) are a class of small non-coding RNAs, which have been demonstrated to play essential roles in plant growth and development, and in responses to abiotic stress. Heat stress is one of the most serious stresses that affecting crop yield and quality, however, the related regulatory mechanisms of miRNAs remains poorly understanding in maize. Results: In this study, a total of 340 miRNAs, including 215 known and 125 novel members, were identified from maize seedlings under heat stress (MH) and control conditions (MC) using high-throughput sequencing approach. The 215 known miRNAs can be further divided into 40 different families, and 21-nt miRNAs were found to be most abundant among the known miRNAs. Thirty-five miRNAs, including 26 known and 9 novel members, were significantly different expressed between MC and MH libraries. Furthermore, 174 target genes were predicted to be cleaved by 115 miRNAs using degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for these targets to explore the biological function and pathways involved. Based on the relationships of miRNAs, target genes and the enriched results, a regulatory network was constructed for the miRNAs and their respective target genes, and 16 significantly differently expressed miRNAs (DEMs) were involved in the network. Conclusions: The results revealed novel insights into the roles of miRNAs in heat stress response and provided a useful foundation for understanding the regulatory mechanisms of heat-responsive miRNAs in maize.

scholarly journals Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dan Liu ◽  
Yanjiao Cui ◽  
Zilong Zhao ◽  
Suying Li ◽  
Dan Liang ◽  
...  
Keyword(s):  
Gene Family ◽  
Molecular Mechanisms ◽  
Profile Analysis ◽  
Foxtail Millet ◽  
Future Studies ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Leaf Tissues ◽  
Identification And Characterization

Abstract Background BES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet. Results In the current study, five common and two unique BES/BZR genes were identified by genome-wide analysis in wheat and foxtail millet, respectively. These genes were unevenly distributed on 14 and five chromosomes of wheat and foxtail millet, respectively, and clustered in two subgroups in a phylogenetic analysis. The BES/BZR gene family members in each subgroup contained similar conserved motifs. Investigation of cis-acting elements and expression profile analysis revealed that the BES/BZR genes were predominantly expressed in leaf tissues of wheat and foxtail millet seedlings and responded to brassinosteroid, abscisic acid, and NaCl treatments. Conclusions Our results provide a basis for future studies on the function and molecular mechanisms of the BES/BZR gene family in wheat, foxtail millet, and other plants.

scholarly journals Transcriptome-wide identification and characterization of the MYB gene family in sickle seagrass (Thalassia hemprichii)

2020 ◽  
Author(s):  
Shen Jie ◽  
Cai Zefu ◽  
Chen Shiquan ◽  
Wang Daoru ◽  
Zhongjie Wu
Keyword(s):  
Aquatic Plants ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Marine Ecology ◽  
Thalassia Hemprichii ◽  
Marine Plants ◽  
Myb Gene ◽  
Important Food Source ◽  
Identification And Characterization

Abstract Background: Sickle seagrass ( Thalassia hemprichii ) is one of the most important marine plants living in the tropical climate, mainly distributed in Southeast Asian waters. It is an important food source for marine herbivores and plays important roles in nitrogen fixation, water purification and maintaining the balance of marine ecology. In recent years, the area of aquatic plants has declined rapidly, affecting the ecological balance. However, the molecular mechanism of aquatic plants has been poorly studied.Results: In this study, all transcriptional information of T. hemprichii was obtained by using high-throughput sequencing technology, and 32,097 unigenes were identified by annotation. In addition, 119 MYB transcription factors were screened, and 61 genes with complete ORF were sequenced. Furthermore, 17 clays were identified according to the information of Arabidopsis .Conclusions: This study provides useful information for enriching the genetic information of T. hemprichii , and further exploring the molecular mechanisms of the evolution, development, and physiological functions of Sickle seagrass.

scholarly journals Gene Expression and miRNA Regulation Changes in Leaves of Rice Backcross Introgression Lines

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1381
Author(s):  
Aqin Cao ◽  
Ruihua Wang ◽  
Jianbo Wang
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Introgression Line ◽  
Differentially Expressed ◽  
Mirna Regulation ◽  
Expression Levels ◽  
Expression Of Genes

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.

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