Identification and Differential Expression of microRNAs in Ovaries of Laying and Broody Geese (Anser cygnoides) by Solexa Sequencing

Xu, Qi; Zhang, Yang; Yang, Chen; Tong, Yiyu; Rong, GuangHui; Huang, Zheng; Zhao, Rongmin; Zhao, Wenming; Wu, Xinsheng; Chang, Guo Bin

doi:10.1371/journal.pone.0087920

Cited by 25 publications

(25 citation statements)

References 40 publications

(49 reference statements)

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“…The sequencing data were analysis as described previously by Xu et al 5 First, the low-quality reads were removed. For the analysis of their distribution, the remaining sequences (clean reads) were mapped to the zebrafish genome using SOAP (http://soap.genomics.org.cn/) with a tolerance of one mismatch.…”

Section: Sequencing Data Analysis and Identification Of Mirnasmentioning

confidence: 99%

“…1 More and more studies have revealed that miRNAs play important roles in many different biological processes, such as proliferation, metabolism, apoptosis, oncogenesis, and immunity. [2][3][4][5] The process of spermatogenesis is very complicated. 6 Recent findings showed that miRNAs were expressed in a developmental stage-specific manner during spermatogenesis, which suggested that these miRNAs might participate in male germ cell development.…”

Section: Introductionmentioning

confidence: 99%

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Identification of MicroRNAs in Zebrafish Spermatozoa

et al. 2015

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MicroRNAs (miRNAs) participate in almost all biological processes. Plenty of evidences show that some testis- or spermatozoa-specific miRNAs play crucial roles in the process of gonad and germ cell development. In this study, the spermatozoa miRNA profiles were investigated through a combination of illumina deep sequencing and bioinformatics analysis in zebrafish. Deep sequencing of small RNAs yielded 11,820,680 clean reads. By mapping to the zebrafish genome, we identified 400 novel and 204 known miRNAs that could be grouped into 104 families. Furthermore, we selected the six highest expressions of known miRNAs to detect their expression patterns in different tissues by stem-loop quantitative real-time polymerase chain reaction. We found that among the six miRNAs, dre-miR-202-5p displayed specific and high expression in zebrafish spermatozoa and testis. Fluorescence in situ hybridization analysis indicated that dre-miR-202-5p was predominantly expressed in all kind of germ cells at different spermatogenetic stages, including spermatogonia and spermatozoa, but barely expressed in the germ cells in the ovary. This sex-biased expression pattern suggests that dre-miR-202-5p might be related to spermatogenesis and the functioning of spermatozoa. The identification of miRNAs in zebrafish spermatozoa and germ cells offers new insights into the spermatogenesis and spermatozoa in the teleost and other vertebrates.

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Section: Sequencing Data Analysis and Identification Of Mirnasmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of MicroRNAs in Zebrafish Spermatozoa

et al. 2015

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“…Another report on miR169 in Arabidopsis found that up‐regulation of the miR169 family initiates stress‐induced early flowering by inhibiting the target gene encoding transcription factor AtNF‐YA (Xu et al . ). The up‐regulated miRNAs, miR398a and miR398b, in the cultivar library are predicted to target RNA binding family (RRM/RBD/RNP) protein genes mediating inhibition through target cleavage.…”

Section: Discussionmentioning

confidence: 97%

“…P ‐value formula:

\begin{matrix} p (x / y) = & {()(, \frac{N_{2}}{N_{1}})}^{y} \frac{(x + y)!}{x! y! {(1 + \frac{N_{2}}{N_{2}})}^{(x + y + 1)}} \\ \begin{matrix} C false(y \leq y_{min} false| x false) = {false\sum}_{y = 0}^{y \leq y_{truemin}} p false(y false| x false) \\ D false(y \leq y_{max} false| x false) = {false\sum}_{y \geq y_{truemax}}^{\infty} p false(y false| x false) \end{matrix} \end{matrix}

where N 1 represent total number of clean reads, x is normalised expression level of the given miRNA from the wild cardamom sRNA library, N 2 total number of clean reads and y is the normalised expression level of a given miRNA in the cultivar sRNA library (Xu et al . ,b).…”

Section: Methodsmentioning

confidence: 99%

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

et al. 2018

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Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.

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“…Many studies have reviewed the critical roles played by miRNAs in controlling the expression of genes essential for folliculogenesis and early embryogenesis11121314. Significant efforts have been made to identify ovarian miRNAs using microarrays or high-throughput sequencing1516171819. However, no comprehensive overview on the ovarian miRNome is available.…”

mentioning

confidence: 99%

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Bouchareb

Cam

Montfort

et al. 2017

Sci Rep

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MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.

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Identification and Differential Expression of microRNAs in Ovaries of Laying and Broody Geese (Anser cygnoides) by Solexa Sequencing

Cited by 25 publications

References 40 publications

Identification of MicroRNAs in Zebrafish Spermatozoa

Identification of MicroRNAs in Zebrafish Spermatozoa

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

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