Identification of miRNAs in sorghum by using bioinformatics approach

Katiyar, Amit; Smita, Shuchi; Chinnusamy, Viswanathan; Pandey, Dev Mani; Bansal, Kailash C.

doi:10.4161/psb.18914

Cited by 39 publications

(17 citation statements)

References 104 publications

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“…Such homologous miRNA families are also typically function-conserved and play essential regulatory roles across plant taxa [17]. Sequence and structure homologies are the central theory of computing-based approaches for miRNA prediction, and many computational methods and protocols have been developed to date [18,19]. We obtained 5943 known mature miRNA sequences from the miRBase (Release 19.0 August 2012) [14] and searched them against the P. dactylifera genome assembly put together by our group.…”

Section: Prediction Of Conserved Mirnas In P Dactylifera Genomementioning

confidence: 99%

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

et al. 2015

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MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.

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Section: Prediction Of Conserved Mirnas In P Dactylifera Genomementioning

confidence: 99%

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

et al. 2015

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“…A bioinformatics pipeline developed by Katiyar et al (2012) using an in-house PERL script and publicly available structure prediction tools could identify 31 new miRNAs representing ten different families from the expressed sequence tags (ESTs) and genomic survey sequence (GSS) available in the public domain. Mapping of newly identified miRNAs (31) and previously known miRNAs (148) on sorghum genome revealed that several MIR genes are arranged in clusters.…”

Section: Microrna (Mirna)mentioning

confidence: 99%

Sorghum Molecular Breeding

Madhusudhana¹,

Rajendrakumar²,

Patil³

2015

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“…Small RNAs are recently emerging group of non‐coding RNAs (Katiyar et al. ), which play important role in gene expression under diverse stress conditions (Das and Mondal ). Several novel small RNAs specific to various abiotic stresses have been discovered either by conventional cloning or by small RNA‐seq analysis (Table ).…”

Section: Small Rna: Non‐coding Genomic Resourcesmentioning

confidence: 99%

Genomic resources for breeding crops with enhanced abiotic stress tolerance

2013

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To meet the challenges of climate change, exploring natural diversity in the existing plant genetic resource pool as well as creation of new mutants through chemical mutagenesis and molecular biology is needed for developing climate-resilient elite genotypes. Ever-increasing area under existing abiotic stresses as well as emerging abiotic stress factors and their combinations have further added to the problems of the current crop improvement programmes. However, with the advancement in modern techniques such as next-generation sequencing technologies, it is now possible to generate on a whole-genome scale, genomic resources for crop species at a much faster pace with considerably less efforts and money. The genomic resources thus generated will be useful for various plant breeding applications such as marker-assisted breeding for gene introgression, mapping QTLs or identifying new or rare alleles associated with a particular trait. In this article, we discuss various aspects of generation of genomic resources and their utilization for developing abiotic stress-tolerant crops to ensure sustainable agricultural production and food security in the backdrop of rapid climate change.

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Identification of miRNAs in sorghum by using bioinformatics approach

Cited by 39 publications

References 104 publications

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

Sorghum Molecular Breeding

Genomic resources for breeding crops with enhanced abiotic stress tolerance

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