scholarly journals Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

2019 ◽  
Vol 20 (20) ◽  
pp. 5122 ◽  
Author(s):  
Paulina Glazińska ◽  
Milena Kulasek ◽  
Wojciech Glinkowski ◽  
Waldemar Wojciechowski ◽  
Jan Kosiński
Keyword(s):  
Small Rna ◽  
Floral Development ◽  
Crop Improvement ◽  
Lupinus Luteus ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Legume Crop ◽  
Yellow Lupine

The floral development in an important legume crop yellow lupine (Lupinus luteus L., Taper cv.) is often affected by the abscission of flowers leading to significant economic losses. Small non-coding RNAs (sncRNAs), which have a proven effect on almost all developmental processes in other plants, might be of key players in a complex net of molecular interactions regulating flower development and abscission. This study represents the first comprehensive sncRNA identification and analysis of small RNA, transcriptome and degradome sequencing data in lupine flowers to elucidate their role in the regulation of lupine generative development. As shedding in lupine primarily concerns flowers formed at the upper part of the inflorescence, we analyzed samples from extreme parts of raceme separately and conducted an additional analysis of pedicels from abscising and non-abscising flowers where abscission zone forms. A total of 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development 59 miRNAs displayed differential expression (DE) and 46 DE miRNAs were found while comparing the upper and lower flowers. Identified tasiR-ARFs were DE in developing flowers and were strongly expressed in flower pedicels. The DEmiR-targeted genes were preferentially enriched in the functional categories related to carbohydrate metabolism and plant hormone transduction pathways. This study not only contributes to the current understanding of how lupine flowers develop or undergo abscission but also holds potential for research aimed at crop improvement.

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.

scholarly journals StarScan: a web server for scanning small RNA targets from degradome sequencing data

2015 ◽  
Vol 43 (W1) ◽  
pp. W480-W486 ◽  
Author(s):  
Shun Liu ◽  
Jun-Hao Li ◽  
Jie Wu ◽  
Ke-Ren Zhou ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
Web Server ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Rna Targets

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 PAREameters: a tool for computational inference of plant miRNA–mRNA targeting rules using small RNA and degradome sequencing data

2020 ◽  
Vol 48 (5) ◽  
pp. 2258-2270 ◽  
Author(s):  
Joshua Thody ◽  
Vincent Moulton ◽  
Irina Mohorianu
Keyword(s):  
Small Rna ◽  
Mirna Target ◽  
Target Prediction ◽  
Model Organisms ◽  
Messenger Rnas ◽  
Mirna Target Prediction ◽  
Sequencing Data ◽  
Translation Rate ◽  
Degradome Sequencing ◽  
Using Data

Abstract MicroRNAs (miRNAs) are short, non-coding RNAs that modulate the translation-rate of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to sequence-specific targets. In plants, this typically results in cleavage and subsequent degradation of the mRNA. Degradome sequencing is a high-throughput technique developed to capture cleaved mRNA fragments and thus can be used to support miRNA target prediction. The current criteria used for miRNA target prediction were inferred on a limited number of experimentally validated A. thaliana interactions and were adapted to fit these specific interactions; thus, these fixed criteria may not be optimal across all datasets (organisms, tissues or treatments). We present a new tool, PAREameters, for inferring targeting criteria from small RNA and degradome sequencing datasets. We evaluate its performance using a more extensive set of experimentally validated interactions in multiple A. thaliana datasets. We also perform comprehensive analyses to highlight and quantify the differences between subsets of miRNA–mRNA interactions in model and non-model organisms. Our results show increased sensitivity in A. thaliana when using the PAREameters inferred criteria and that using data-driven criteria enables the identification of additional interactions that further our understanding of the RNA silencing pathway in both model and non-model organisms.

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 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 transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid biosynthesis in leafy sweet potato

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245266
Author(s):  
Yi Liu ◽  
Wenjin Su ◽  
Lianjun Wang ◽  
Jian Lei ◽  
Shasha Chai ◽  
...  
Keyword(s):  
Chlorogenic Acid ◽  
Sweet Potato ◽  
Small Rna ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Ethylene Response Factor ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Phenylpropanoid Biosynthesis

Leafy sweet potato is rich in total phenolics (TP) which play key roles in health protection, the chlorogenic acid (CGA) constitutes the major components of phenolic compounds in leafy sweet potato. Unfortunately, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. To dissect the mechanisms of CGA biosynthesis, we performed transcriptome, small RNA (sRNA) and degradome sequencing of one low-CGA content and one high-CGA content genotype at two stages. A total of 2,333 common differentially expressed genes (DEGs) were identified, and the enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. The functional genes, such as CCR, CCoAOMT and HCT in the CGA biosynthetic pathway were down-regulated, indicating that the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. A total of 38 DE miRNAs were identified, and 1,799 targets were predicated for 38 DE miRNAs by using in silico approaches. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2/ethylene response factor (AP2/ERF) and Squamosa promoter binding protein-like (SPL) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family negatively targeted AP2/ERF and SPL. Six mRNAs and six miRNAs were validated by qRT-PCR, and the results showed that the expression levels of the mRNAs and miRNAs were consistent with the sequencing data. This study established comprehensive functional genomic resources for the CGA biosynthesis, and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs, and offered candidate genes for leafy sweet potato improvements.

scholarly journals Transcriptome analysis in the shell gland of laying hens affecting eggshell qualities

2020 ◽  
Author(s):  
Xinyue Yang ◽  
Fuping Zhao ◽  
Qiqi Han ◽  
Yuanyang Dong ◽  
Jiaqi Lei ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Laying Hens ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Shell Gland ◽  
Sequencing Data ◽  
Physical Damage ◽  
Eggshell Quality ◽  
Dietary Nutrient ◽  
Gland Development

Abstract Background Eggshell plays an important role in protecting against physical damage and microorganic invasion. It is subject to quality loss with increasing hen age, and fragile eggshells result in huge economic losses to the poultry industry. Therefore, improving eggshell quality is particularly important. However, little is known about the potential molecular mechanisms regulating eggshell quality in chickens. Methods In this study, we aimed to compare differential expression of long non-coding RNAs (lncRNAs) and mRNAs between old and young laying hens to identify related candidate genes for chicken shell gland development by the method of high-throughput RNA sequencing (RNA-seq). Results In total, we detected 176 and 383 differentially expressed (DE) lncRNAs and mRNAs, respectively. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases revealed that DE-lncRNAs and DE-mRNAs were significantly enriched in “phosphate-containing compound metabolic process”, “mitochondrial proton-transporting ATP synthase complex”, “inorganic anion transport”, and other terms related to eggshell calcification and cuticularization. Through integrated analysis, we found that some important genes such as FGF14, COL25A1, GPX8, and GRXCR1 and their corresponding lncRNAs were expressed differentially between two groups, and the results of quantitative real-time polymerase chain reaction (qPCR) among these genes were also in excellent agreement with the sequencing data. In addition, our research indicates that FGF14, COL25A1, GPX8, and the members of the SLC family may be key genes that affect eggshell quality in hens. Conclusions This study provides a catalog of lncRNAs and mRNAs of the laying hen eggshell gland and will contribute to a fuller understanding of the molecular mechanisms of the function of the shell gland in poultry. Our findings will provide a valuable reference for the development of breeding programs aimed at breeding excellent poultry with high eggshell quality or regulating dietary nutrient levels to improve eggshell quality.

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