title: Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags.
abstract: The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
authors.forename: Debashis
authors.initials: D
authors.lastname: Panda
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
authors.forename: Budheswar
authors.initials: B
authors.lastname: Dehury
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
authors.forename: Jagajjit
authors.initials: J
authors.lastname: Sahu
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
authors.forename: Madhumita
authors.initials: M
authors.lastname: Barooah
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
authors.forename: Priyabrata
authors.initials: P
authors.lastname: Sen
authors.affiliation: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India. Electronic address: mkmodi@gmail.com.
authors.forename: Mahendra K
authors.initials: MK
authors.lastname: Modi
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D005737:Garlic / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D035683:MicroRNAs
keywords: Comparative genomics; EST; Expressed sequence tag (EST); GSS; Garlic; MFE; MFEI; expressed sequence tag; genome survey sequence; miRNA; microRNA; minimal folding free energy; minimal folding free energy index; plant small RNA target analysis server; psRNATarget; psRNAtarget server; qRT-PCR; quantitative real-time polymerase chain reaction