Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169

Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO2 supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO2 revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs’ target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.

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Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

BMC Plant Biology ◽

10.1186/s12870-021-02835-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Guoning Wang ◽

Xingfen Wang ◽

Yan Zhang ◽

Jun Yang ◽

Zhikun Li ◽

...

Keyword(s):

Disease Resistance ◽

Verticillium Wilt ◽

Dynamic Characteristics ◽

Target Genes ◽

Acid Metabolism ◽

Expression Profiles ◽

Enrichment Analysis ◽

Alpha Linolenic Acid ◽

Non Coding Rna ◽

Long Non Coding Rna

Abstract Background Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. Results Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. Conclusion This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

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

10.21203/rs.3.rs-44831/v1 ◽

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.

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Characterization of Putative Effectors from the Cereal Cyst Nematode Heterodera avenae

Phytopathology ◽

10.1094/phyto-07-17-0226-r ◽

2018 ◽

Vol 108 (2) ◽

pp. 264-274 ◽

Cited By ~ 4

Author(s):

Jiang-Kuan Cui ◽

Huan Peng ◽

Fen Qiao ◽

Gao-Feng Wang ◽

Wen-Kun Huang ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Developmental Stages ◽

Heterodera Avenae ◽

Parasitic Nematodes ◽

Sequencing Analysis ◽

Rnai Technology

Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant-parasitic nematodes that play an important role in the invasion process. A total of 1,480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.

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Transcriptome analysis identified long non-coding RNAs involved in the adaption of yak to high-altitude environments

Royal Society Open Science ◽

10.1098/rsos.200625 ◽

2020 ◽

Vol 7 (9) ◽

pp. 200625

Author(s):

Jin-Wei Xin ◽

Zhi-Xin Chai ◽

Cheng-Fu Zhang ◽

Yu-Mei Yang ◽

Qiang Zhang ◽

...

Keyword(s):

Muscle Contraction ◽

High Altitude ◽

Target Genes ◽

Calcium Release ◽

Phosphoglycerate Mutase ◽

Acid Oxidation ◽

Transcriptional Level ◽

Calcium Release Channel ◽

Release Channel ◽

Kegg Pathways

The mechanisms underlying yak adaptation to high-altitude environments have been investigated using various methods, but no report has focused on long non-coding RNA (lncRNA). In the present study, lncRNAs were screened from the gluteus transcriptomes of yak and their transcriptional levels were compared with those in Sanjiang cattle, Holstein cattle and Tibetan cattle. The potential target genes of the differentially expressed lncRNAs between species/strains were predicted using cis and trans models. Based on cis -regulated target genes, no KEGG pathway was significantly enriched. Based on trans -regulated target genes, 11 KEGG pathways in relation to energy metabolism and three KEGG pathways associated with muscle contraction were significantly enriched. Compared with cattle strains, transcriptional levels of acyl-CoA dehydrogenase, acyl-CoA-binding protein, 3-hydroxyacyl-CoA dehydrogenase were relatively higher and those of glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate mutase 1, pyruvate kinase and lactate/malate dehydrogenase were relatively lower in yak, suggesting that yaks activated fatty acid oxidation but inhibited glucose oxidation and glycolysis. Besides, NADH dehydrogenase and ATP synthase showed lower transcriptional levels in yak than in cattle, which might protect muscle tissues from deterioration caused by reactive oxygen species (ROS). Compared with cattle strains, the higher transcriptional level of glyoxalase in yak might contribute to dicarbonyl stress resistance. Voltage-dependent calcium channel/calcium release channel showed a lower level in yak than in cattle strains, which could reduce the Ca 2+ influx and subsequently decrease the risk of hypertension. However, levels of EF-hand and myosin were higher in yak than in cattle strains, which might enhance the negative effects of reduced Ca 2+ on muscle contraction. Overall, the present study identified lncRNAs and proposed their potential regulatory functions in yak.

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Characterization of microRNA Profiles in Pasteurella multocida-Infected Rabbits and Identification of miR-29-5p as a Regulator of Antibacterial Immune Response

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.746638 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jiaqing Hu ◽

Wenqiang Li ◽

Xibo Qiao ◽

Wenjie Li ◽

Kerui Xie ◽

...

Keyword(s):

Immune Response ◽

Pasteurella Multocida ◽

Target Genes ◽

Expression Patterns ◽

Rabbit Lung ◽

T Box ◽

Kegg Pathways ◽

Small Rna Deep Sequencing ◽

Epithelial Membrane Protein 2

Pasteurella multocida is the pathogenic agent for a variety of severe diseases in livestock, including rabbits. MicroRNAs (miRNAs) participate in the immune response to the pathogen. Distinct miRNA expression patterns were explored in rabbit lung by small-RNA deep sequencing to assess dysregulated miRNAs during P. multocida infection. Totally, 571 miRNAs were screened, of which, 62 were novel, and 32 exhibited differential expression (DE). Of the 32 known DE-miRNAs, 13 and 15 occurred at 1 day and 3 days post-infection (dpi); and ocu-miR-107-3p and ocu-miR-29b-5p were shared between the two time points. Moreover, 7,345 non-redundant target genes were predicted for the 32 DE-miRNAs. Putative target genes were enriched in diverse GO and KEGG pathways and might be crucial for disease resistance. Interestingly, upregulation of ocu-miR-29-5p suppresses P. multocida propagation and downregulates expression of epithelial membrane protein-2 (EMP2) and T-box 4 (TBX4) genes by binding to their 3′ untranslated region in RK13 cells. Thus, ocu-miR-29-5p may indirectly inhibit P. multocida invasion by modulating genes related to the host immune response, such as EMP2 and TBX4.

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Contribution Value：A Indicator for Measuring the Contribution of ncRNAs to Transcriptome

10.21203/rs.3.rs-32442/v1 ◽

2020 ◽

Author(s):

Xinyi Gu ◽

Bo Jin ◽

Zhidan Qi ◽

Xiaofeng Yin

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Enrichment Analysis ◽

P Value ◽

Data Sets ◽

Kegg Pathways ◽

Multiple Data ◽

C Value ◽

Multiple Data Sets ◽

Main Basis

Abstract Background：The expression difference multiple log2 FC and P value are often the main basis for screening ncRNA after high-throughput sequencing. However, the above two indicators can’t well reflect the regulatory effect of nonprotein coding RNA (ncRNA) on mRNA. Therefore, we propose a new indicator, Contribution value (C value), to characterize the contribution of ncRNAs to transcriptome transformation.Results：In this study, we analyzed multiple data sets from mice and humans. We take all differential expression mRNAs as a parent set and the GO and KEGG enrichment analysis were performed on it. C value can be simply regarded as the sum of the product of the richfactor of each ncRNA target genes participating in each term/pathway and the P value of that term/pathway obtained from the parent set. We found that C value was superior to log2 FC and P value in all operation results.Conclusions：We show that the C value, which takes into accounts the the KEGG pathways and GO terms involved in the development of the disease, provides a measure of another dimension compared with the log2FC and P value. These hidden interactions between ncRNAs and their target genes may provide more comprehensive analysis.

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De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing

Genetics Research International ◽

10.1155/2015/638679 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Bhaskar Reddy ◽

Amrutlal K. Patel ◽

Krishna M. Singh ◽

Deepak B. Patil ◽

Pinesh V. Parikh ◽

...

Keyword(s):

High Throughput Sequencing ◽

De Novo ◽

Open Reading Frames ◽

Dinucleotide Repeats ◽

Kegg Pathways ◽

Ion Torrent Pgm ◽

Retinal Tissue ◽

Retinol Metabolism ◽

And Function

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.

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Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Animals ◽

10.3390/ani10091633 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1633

Author(s):

Yi Wang ◽

Zhigang Niu ◽

Zhengcheng Zeng ◽

Yao Jiang ◽

Yifan Jiang ◽

...

Keyword(s):

Signaling Pathway ◽

Acid Metabolism ◽

Snp Array ◽

Enrichment Analysis ◽

Smooth Muscle Contraction ◽

Potential Candidate ◽

Alpha Linolenic Acid ◽

Hormone Synthesis ◽

Sheep Breeds ◽

Kegg Pathways

Selection signature provides an efficient tool to explore genes related to traits of interest. In this study, 176 ewes from one Chinese uniparous breed and three Kazakhstan multiparous breeds are genotyped using Affymetrix 600K HD single nucleotide polymorphism (SNP) arrays, F-statistics (Fst), and a Cross Population Extend Haplotype Homozygosity Test (XPEHH). These are conducted to identify genomic regions that might be under selection in three population pairs comprised the one multiparous breed and the uniparous breed. A total of 177 and 3072 common selective signatures were identified by Fst and XPEHH test, respectively. Nearly half of the common signatures detected by Fst were also captured by XPEHH test. In addition, 1337 positive and 1735 common negative signatures were observed by XPEHH in three Kazakhstan multiparous breeds. In total, 242 and 798 genes were identified in selective regions and positive selective regions identified by Fst and XPEHH, respectively. These genes were further clustered in 50 gene ontology (GO) functional terms and 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis. The GO terms and pathways were relevant with reproductive processes, e.g., oxytocin signaling pathway, thyroid hormone synthesis and GnRH signaling pathway, vascular smooth muscle contraction and lipid metabolism (alpha-Linolenic acid metabolism and Linoleic acid metabolism), etc. Based on the findings, six potential candidate genes ESR1, OXTR, MAPK1, RYR1, PDIA4, and CYP19A1, under positive selection related to characteristics of multiparous sheep breeds were revealed. Our results improve our understanding of the mechanisms of selection that underlies the prolificacy trait in sheep, and provide essential references for future sheep breeding.

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

BMC Genomics ◽

10.1186/s12864-020-07272-9 ◽

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.

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The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges

Microorganisms ◽

10.3390/microorganisms9020442 ◽

2021 ◽

Vol 9 (2) ◽

pp. 442

Author(s):

Mouna Hamel ◽

Jean-Marc Rolain ◽

Sophie Alexandra Baron

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Resistance Mechanisms ◽

Published Data ◽

Bacterial Strains ◽

Colistin Resistance ◽

Advanced Technologies ◽

History Of ◽

Efficient Exploration

Since 2015, the discovery of colistin resistance genes has been limited to the characterization of new mobile colistin resistance (mcr) gene variants. However, given the complexity of the mechanisms involved, there are many colistin-resistant bacterial strains whose mechanism remains unknown and whose exploitation requires complementary technologies. In this review, through the history of colistin, we underline the methods used over the last decades, both old and recent, to facilitate the discovery of the main colistin resistance mechanisms and how new technological approaches may help to improve the rapid and efficient exploration of new target genes. To accomplish this, a systematic search was carried out via PubMed and Google Scholar on published data concerning polymyxin resistance from 1950 to 2020 using terms most related to colistin. This review first explores the history of the discovery of the mechanisms of action and resistance to colistin, based on the technologies deployed. Then we focus on the most advanced technologies used, such as MALDI-TOF-MS, high throughput sequencing or the genetic toolbox. Finally, we outline promising new approaches, such as omics tools and CRISPR-Cas9, as well as the challenges they face. Much has been achieved since the discovery of polymyxins, through several innovative technologies. Nevertheless, colistin resistance mechanisms remains very complex.

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