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

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.

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

10.21203/rs.3.rs-31410/v1 ◽

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.

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

Biomolecules ◽

10.3390/biom9090483 ◽

2019 ◽

Vol 9 (9) ◽

pp. 483 ◽

Cited By ~ 1

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.

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

BMC Genomics ◽

10.1186/1471-2164-15-25 ◽

2014 ◽

Vol 15 (1) ◽

pp. 25 ◽

Cited By ~ 62

Author(s):

Hongjun Liu ◽

Cheng Qin ◽

Zhe Chen ◽

Tao Zuo ◽

Xuerong Yang ◽

...

Keyword(s):

Small Rna ◽

Target Genes ◽

Degradome Sequencing

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.742347 ◽

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.

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

10.21203/rs.2.9588/v1 ◽

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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Identification of miRNAs and Their Target Genes Associated with Sweet Corn Seed Vigor by Combined Small RNA and Degradome Sequencing

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.5b00522 ◽

2015 ◽

Vol 63 (22) ◽

pp. 5485-5491 ◽

Cited By ~ 5

Author(s):

Shumin Gong ◽

Yanfei Ding ◽

Shanxia Huang ◽

Cheng Zhu

Keyword(s):

Small Rna ◽

Target Genes ◽

Sweet Corn ◽

Seed Vigor ◽

Corn Seed ◽

Degradome Sequencing

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

PLoS ONE ◽

10.1371/journal.pone.0245266 ◽

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.

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

10.21203/rs.2.14343/v3 ◽

2020 ◽

Author(s):

Yi Liu ◽

Wenjin Su ◽

Lianjun Wang ◽

Jian Lei ◽

Shasha Chai ◽

...

Keyword(s):

Phenolic Compounds ◽

Chlorogenic Acid ◽

Sweet Potato ◽

Small Rna ◽

In Silico ◽

Molecular Mechanisms ◽

Target Genes ◽

Ethylene Response Factor ◽

Degradome Sequencing ◽

Dicaffeoylquinic Acid

Abstract Background: Phenolic compounds play key roles in health protection and leafy sweet potato is an excellent source of total phenolics (TP). The chlorogenic acid (CGA) family, which includes caffeoylquinic acid (CQA), 3,4-O-dicaffeoylquinic acid (3,4-diCQA), 3,5-O-dicaffeoylquinic acid (3,5-diCQA) and 4,5-O-dicaffeoylquinic acid (4,5-diCQA) , constitutes the major components of phenolic compounds in leafy sweet potato. However, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. The objective of present study is to dissect the mechanisms of CGA biosynthesis by using transcriptome, small RNA (sRNA) and degradome sequencing. Results: Transcriptome sequencing of twelve samples (triple replicates) from one low-CGA content genotype and one high-CGA content genotype at two stages (65 and 85 days after planting) identified a total of 2333 common differentially expressed genes (DEGs). The enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. In this study, functional genes CCR , CCoAOMT and HCT in the CGA biosynthetic pathway were uniformly downregulated, indicating the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. The sRNA sequencing identified a total of 38 DE miRNAs. Using in silico approaches, 1799 targets were predicated for 38 DE miRNAs. 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 targeted DHQ / SDH (3-dehydroquinate dehydratase/shikimate dehydrogenase), the key gene in the phenylpropanoid pathway. Conclusions: 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 improvement s.

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