High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

Wang, Yanmei; Ding, Yan; Yu, Dingli; Wei, Xin; Liu, Jinyuan

doi:10.1007/s11427-015-4877-5

Cited by 11 publications

(10 citation statements)

References 25 publications

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“…It has been reported that most sRNAs functioning as small interfering RNAs (siRNAs) are 24 nt long (Rajagopalan et al, 2006); the appearance of such large numbers of 24 nt sRNAs in the four small RNA libraries indicated that siRNAs accounted for a large proportion in the sRNA datasets. These results are in agreement with previous reports on cotton (Wang et al, 2015) and other plants such as rice (Li et al, 2011), maize (Kang et al, 2012), and Medicago truncatula (Szittya et al, 2008). …”

Section: Resultssupporting

confidence: 94%

“…Advances in the understanding of miRNA-mediated gene regulation revealed that miRNAs play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction (Jones-Rhoades et al, 2006; Li and Zhang, 2016). To date, several studies have investigated many miRNAs and their regulatory functions in the developmental processes of cotton fibers (Wang et al, 2012, 2015; Xue et al, 2013; Liu et al, 2014; Yu et al, 2014; Xie et al, 2015). Both computational prediction and experimental examinations have been widely employed to identify miRNAs in plants.…”

Section: Introductionmentioning

confidence: 99%

“…Subsequently, eight fiber elongation-related miRNAs were identified in the genome of G. raimondii Ulbr (Xue et al, 2013). Recently, 21 novel miRNA candidates were found to be expressed in secondary wall thickening fiber cells (Yu et al, 2014) and 23 novel miRNAs were identified in developing cotton seeds (Wang et al, 2015). To date, a total of 713 and 427 miRNAs have been identified in the model plant species Oryza sativa and Arabidopsis thaliana , respectively.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing

2016

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Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families. Furthermore, RLM-5′ RACE (RNA ligase-mediated rapid amplification of 5′-cDNA ends) experiments identified the targets of eight important miRNAs, and the expression levels of these target genes were confirmed to be negatively correlated with the expression patterns of their corresponding miRNAs. We propose a potential functional network mediated through these eight miRNAs to illustrate their important functions in fiber elongation. Our study provides novel insights into the dynamic profiles of these miRNAs and a basis for investigating the regulatory mechanisms involved in the elongation of cotton fibers.

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Section: Resultssupporting

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing

2016

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“…(2012) detected 125 and 127 known miRNAs in maize seeds and leaves, respectively20; and Wang et al . (2015) discovered 95 known miRNAs and 23 novel miRNA candidates in cotton seeds30. Here, in our study, 94 known and 3 novel miRNAs were identified in C. gynandra , and 102 known and 3 novel miRNAs were identified in C. hassleriana .…”

Section: Discussionsupporting

confidence: 56%

Identification and characterization of miRNAs in two closely related C4 and C3 species of Cleome by high-throughput sequencing

Gao

Zhao

et al. 2017

Sci Rep

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Cleome gynandra and Cleome hassleriana, which are C4 and C3 plants, respectively, are two species of Cleome. The close genetic relationship between C. gynandra and C. hassleriana provides advantages for discovering the differences in leaf development and physiological processes between C3 and C4 plants. MicroRNAs (miRNAs) are a class of important regulators of various biological processes. In this study, we investigate the differences in the characteristics of miRNAs between C. gynandra and C. hassleriana using high-throughput sequencing technology. In total, 94 and 102 known miRNAs were identified in C. gynandra and C. hassleriana, respectively, of which 3 were specific for C. gynandra and 10 were specific for C. hassleriana. Ninety-one common miRNAs were identified in both species. In addition, 4 novel miRNAs were detected, including three in C. gynandra and three in C. hassleriana. Of these miRNAs, 67 were significantly differentially expressed between these two species and were involved in extensive biological processes, such as glycol-metabolism and photosynthesis. Our study not only provided resources for C. gynandra and C. hassleriana research but also provided useful clues for the understanding of the roles of miRNAs in the alterations of biological processes in leaf tissues during the evolution of the C4 pathway.

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“…Sequencing was done on the Illumina platform generating paired end reads of 100 bp each. Raw reads were filtered and trimmed based on quality and adapter inclusion using the SOAPnuke 1.5.0 software (http://soap.genomics.org.cn/) [62]. After filtering, the remaining reads are called ‘clean reads’ and stored in FASTQ.…”

Section: Methodsmentioning

confidence: 99%

De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress

Miao

Shao

et al. 2016

BMC Genomics

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Background Elymus nutans Griseb., is an important alpine perennial forage of Pooideae subfamily with strong inherited cold tolerance. To get a deeper insight into its molecular mechanisms of cold tolerance, we compared the transcriptome profiling by RNA-Seq in two genotypes of Elymus nutans Griseb. the tolerant Damxung (DX) and the sensitive Gannan (GN) under cold stress.ResultsThe new E. nutans transcriptomes were assembled and comprised 200,520 and 181,331 transcripts in DX and GN, respectively. Among them, 5436 and 4323 genes were differentially expressed in DX and GN, with 170 genes commonly expressed over time. Early cold responses involved numerous genes encoding transcription factors and signal transduction in both genotypes. The AP2/EREBP famliy of transcription factors was predominantly expressed in both genotypes. The most significant transcriptomic changes in the later phases of cold stress are associated with oxidative stress, primary and secondary metabolism, and photosynthesis. Higher fold expressions of fructan, trehalose, and alpha-linolenic acid metabolism-related genes were detected in DX. The DX-specific dehydrins may be promising candidates to improve cold tolerance. Twenty-six hub genes played a central role in both genotypes under cold stress. qRT-PCR analysis of 26 genes confirmed the RNA-Seq results.ConclusionsThe stronger transcriptional differentiation during cold stress in DX explains its better cold tolerance compared to GN. The identified fructan biosynthesis, alpha-linolenic acid metabolism, and DX-specific dehydrin-related genes may provide genetic resources for the improvement of cold-tolerant characters in DX. Our findings provide important clues for further studies of the molecular mechanisms underlying cold stress responses in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3222-0) contains supplementary material, which is available to authorized users.

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High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

Cited by 11 publications

References 25 publications

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing

Identification and characterization of miRNAs in two closely related C4 and C3 species of Cleome by high-throughput sequencing

De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress

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