scholarly journals miRNA and Degradome Sequencing Reveal miRNA and Their Target Genes That May Mediate Shoot Growth in Spur Type Mutant “Yanfu 6”

2017 ◽  
Vol 8 ◽  
Author(s):  
Chunhui Song ◽  
Dong Zhang ◽  
Liwei Zheng ◽  
Jie Zhang ◽  
Baojuan Zhang ◽  
...  
Keyword(s):  
Shoot Growth ◽  
Target Genes ◽  
Degradome Sequencing ◽  
Type Mutant

Small RNA, transcriptome, and degradome sequencing to identify salinity stress responsive miRNAs and target genes in Dunaliella salina

2018 ◽  
Vol 31 (2) ◽  
pp. 1175-1183 ◽  
Author(s):  
Xiangnan Gao ◽  
Yuting Cong ◽  
Jinrong Yue ◽  
Zhenyu Xing ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Small Rna ◽  
Dunaliella Salina ◽  
Target Genes ◽  
Degradome Sequencing

scholarly journals Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing

2021 ◽  
Vol 22 (18) ◽  
pp. 10154
Author(s):  
Tengfei Shen ◽  
Mengxuan Xu ◽  
Haoran Qi ◽  
Yuanheng Feng ◽  
Zhangqi Yang ◽  
...  
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Higher Plants ◽  
Raw Materials ◽  
Pinus Massoniana ◽  
Wood Formation ◽  
Mineral Elements ◽  
Small Rna Sequencing ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species.

scholarly journals Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

2020 ◽  
Author(s):  
Xiao-Meng Liu ◽  
Shui-Yuan Cheng ◽  
Jia-Bao Ye ◽  
Ze-Xiong Chen ◽  
Yong-Ling Liao ◽  
...  
Keyword(s):  
Small Rna ◽  
Ginkgo Biloba ◽  
Sexual Differentiation ◽  
Target Genes ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Multiple Perspectives ◽  
Juvenile Period ◽  
Degradome Sequencing ◽  
Screening And Identification

Abstract Background: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties.Results: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3,293 miRNAs were identified in buds and strobili of G. biloba, including 1,085 conserved miRNAs and 2,208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4,346 and 7,087 differentially expressed genes (DEGs) in MB _vs_ FB and MS _vs_ OS, respectively. A total of 6,032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identified 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. Conclusions: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

scholarly journals miR8181 is Involved in the Cell Growth and Development Regulation of Saccharina Japonica

2020 ◽  
Author(s):  
Xiaoqi Yang ◽  
Xiu liang Wang ◽  
Jian ting Yao ◽  
Wei Li ◽  
Delin Duan
Keyword(s):  
Transcriptional Regulation ◽  
Cell Growth ◽  
Blue Light ◽  
Cleavage Site ◽  
Growth And Development ◽  
Target Genes ◽  
Saccharina Japonica ◽  
Degradome Sequencing ◽  
Post Transcriptional Regulation ◽  
Development Regulation

Abstract Background: Aureochrome, a blue-light receptor found in photosynthetic stramenopiles, plays an important role in brown algal growth and development. Aureochrome preserves the reversed effector-sensor domain for blue light reception and acts as the candidate optogenetic tool for light induced post-transcriptional regulation, but the inner rapid regulation of aureochrome remains to be studied. MicroRNA (miRNAs) of plant can cleavage the specific base-pairing site of mRNA by RNA interference mechanism, and such post-transcriptional regulation of miRNAs to photoreceptor has received attention due to the flexible regulation pathway. However, the targeting relationship between aureochrome and miRNA is unclear.Results: In this study, the potential regulatory network between miRNAs and aureochrome were explored by transcriptome and sRNA sequencing in Saccharina japonica. Our results found that 18 miRNAs perfectly paired with aureochrome. Among the screened miRNAs, miR8181-x was negatively correlated with aureochrome5 with high credibility and exhibited tissue-specific expression in S. japonica. Degradome sequencing detected the exact cleavage site of miR8181-x on aureochrome5, confirming their targeting regulation relationship. Among the 54 target genes of miR8181-x, nine genes of ABC transporters, E3 ubiquitin-protein protein ligase, Hsp90, Mx1, PetC, EF2, GSA, HAD-superfamily hydrolase and SET2 that exhibited similar expression with aureochrome5 competed with the same binding site, thus constructing the competing endogenous RNA network. Functional analysis of miR8181-x target genes revealed that regulation of cell differentiation and development was enriched, indicating the potential role of miR8181-x in the regulation of growth and development.Conclusion: Our study found that miR8181-x negatively regulated the expression of aureochrome5. The exact cleavage site in aureochrome5 were verified by degradome sequencing, confirming the targeting relationships. Functional enrichment of miR8181-x target genes revealed that miR8181-x involved in the cell growth and development regulation of S. japonica.

scholarly journals Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 483 ◽  
Author(s):  
Sun ◽  
Luo ◽  
Chang ◽  
Li ◽  
Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Complex Biological Process ◽  
Cucumber Fruit ◽  
Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

scholarly journals Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 25 ◽  
Author(s):  
Hongjun Liu ◽  
Cheng Qin ◽  
Zhe Chen ◽  
Tao Zuo ◽  
Xuerong Yang ◽  
...  
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Degradome Sequencing

scholarly journals Integrated Analysis of MicroRNA and Target Genes in Brachypodium distachyon Infected by Magnaporthe oryzae by Small RNA and Degradome Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Weiye Peng ◽  
Na Song ◽  
Wei Li ◽  
Mingxiong Yan ◽  
Chenting Huang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Small Rna ◽  
Target Genes ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Integrated Analysis ◽  
Post Inoculation ◽  
New Approach ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas

Rice blast caused by Magnaporthe oryzae is one of the most important diseases that seriously threaten rice production. Brachypodium distachyon is a grass species closely related to grain crops, such as rice, barley, and wheat, and has become a new model plant of Gramineae. In this study, 15 small RNA samples were sequenced to examine the dynamic changes in microRNA (miRNA) expression in B. distachyon infected by M. oryzae at 0, 24, and 48 h after inoculation. We identified 432 conserved miRNAs and 288 predicted candidate miRNAs in B. distachyon. Additionally, there were 7 and 19 differentially expressed miRNAs at 24 and 48 h post-inoculation, respectively. Furthermore, using degradome sequencing, we identified 2,126 genes as targets for 308 miRNAs; using quantitative real-time PCR (qRT-PCR), we validated five miRNA/target regulatory units involved in B. distachyon–M. oryzae interactions. Moreover, using co-transformation technology, we demonstrated that BdNAC21 was negatively regulated by miR164c. This study provides a new approach for identifying resistance genes in B. distachyon by mining the miRNA regulatory network of host–pathogen interactions.

scholarly journals Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

2019 ◽  
Author(s):  
Paulina Glazinska ◽  
Milena Kulasek ◽  
Wojciech Glinkowski ◽  
Waldemar Wojciechowski ◽  
Jan Kosiński
Keyword(s):  
Information Processing ◽  
Small Rna ◽  
Target Genes ◽  
Signal Transduction Pathway ◽  
Lupinus Luteus ◽  
Integrated Analysis ◽  
Degradome Sequencing ◽  
Kegg Pathways ◽  
Legume Crop ◽  
Yellow Lupine

Abstract Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

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