Conserved miRNAs and their targets identified in lettuce (Lactuca) by EST analysis

Han, Yousheng; Zhu, Beiwei; Luan, Fulei; Zhu, Hongliang; Shao, Yi; Chen, Anjun; Lü, Chao; Luo, Yunbo

doi:10.1016/j.gene.2010.04.012

Cited by 19 publications

(10 citation statements)

References 39 publications

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“…Since miRNA precursors are transcribed by RNA polymerase II and polyadenylated (Lee et al 2004), some pre-miRNAs should be represented by expressed sequence tags (EST). EST analysis (Zhang et al 2005) is widely used in model plants and species with limited genomic resources (Han et al 2010; Colaiacovo et al 2010; Bhardwaj et al 2010; Kim et al 2011). The EST approach is usually based on a sequence similarity search step followed by a set of structural filters.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

Chao

Jean

et al. 2013

Plant Mol Biol

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Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5′ ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0150-0) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

Chao

Jean

et al. 2013

Plant Mol Biol

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“…Comparative genome-based computational approaches have been used to identify hundreds of miRNAs in a variety of plants including cotton (Qiu et al 2007;Zhang et al 2007), soybean (Zhang et al 2008a), maize (Zhang et al 2006b), rice (Lu et al 2005), wheat (Yin and Shen 2010), tomato (Yin et al 2008;Zhang et al 2008b), potato Zhang et al 2009), oil rape , citrus ), lettuce (Han et al 2010), apple (Gleave et al 2008), Brachypodium distachyon (Unver and Budak 2009), and Populus euphratica ). This method has been preferred over experimental approaches, such as direct cloning and deep sequencing, for two reasons.…”

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confidence: 99%

Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)

Frazier

Xie

Freistaedter

et al. 2010

Planta

114

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microRNAs (miRNAs) are a recently discovered class of small (~21 nt) endogenous gene regulators that have been shown to play an important role in plant growth and development by aiding in organ maturation, hormone signaling, tissue differentiation, and plant tolerance to environmental stress. Since a list of miRNAs has never been generated for tobacco, we employed genome survey sequence analysis to computationally identify 259 potentially conserved tobacco miRNAs, belonging to 65 families, and validated 11 of these miRNAs using qRT-PCR. The 65 miRNA families were dramatically different in size. miRNA precursor (pre-miRNA) sequence analysis showed that tobacco pre-miRNAs greatly varied from 45 to 635 nt in length with an average of 141 ± 108 nt. We were also able to determine the presence of antisense miRNAs as well as miRNA clusters in tobacco. Using previously established protocols, a total of 1,225 potential target genes were predicted for the newly identified tobacco miRNAs. These target genes include transcription factors, DNA replication proteins, metabolic enzymes, as well as other gene targets necessary for proper plant maturation. The results of this study show that conserved miRNAs exist in tobacco and suggest that these miRNAs may play an important role in tobacco growth and development.

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“…To date, numerous miRNAs have been identified by EST analysis strategy from various plant species such as apple, cabbage, citrus, coffee, cucurbit, garlic, lettuce, peach, potato, radish, strawberry, sweet potato, etc. [18][19][20][21][22][23][24][25][26][27][28][29] Blueberry is an economically important small fruit crop. Blueberry fruit is rich in anthocyanins, which have been associated with many recognized health benefits including improvement of night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease.…”

Section: Introductionmentioning

confidence: 99%

Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum)

Hou

Zhang

et al. 2014

Plant Signaling & Behavior

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MicroRNas (miRNas) are a class of endogenous, approximately 21nt in length, non-coding RNa, which mediate the expression of target genes primarily at post-transcriptional levels. miRNas play critical roles in almost all plant cellular and metabolic processes. although numerous miRNas have been identified in the plant kingdom, the miRNas in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNas and their targets in blueberry. By conducting an esT-based comparative genomics approach, 9 potential vco-miRNas were discovered from 22,402 blueberry esTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNa and its target transcript, 34 target esTs from blueberry and 70 targets from other species were identified for the vcomiRNas. The targets were found to be involved in transcription, RNa splicing and binding, DNa duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNas.

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Conserved miRNAs and their targets identified in lettuce (Lactuca) by EST analysis

Cited by 19 publications

References 39 publications

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)

Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum)

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