In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs).
The endogenous small non-coding micro RNAs (miRNAs), which are typically ~21-24 nt nucleotides, play a crucial role in regulating the intrinsic normal growth of cells and development of the plants as well as in maintaining the integrity of genomes. These small non-coding RNAs function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets, and further inferring miRNA functions is a routine process to understand normal biological processes of miRNAs and their roles in the development of plants. Comparative genomics based approach using expressed sequence tags (EST) and genome survey sequences (GSS) offer a cost-effective platform for identification and characterization of miRNAs and their target genes in plants. Despite the fact that sweet potato (Ipomoea batatas L.) is an important staple food source for poor small farmers throughout the world, the role of miRNA in various developmental processes remains largely unknown. In this paper, we report the computational identification of miRNAs and their target genes in sweet potato from their ESTs. Using comparative genomics-based approach, 8 potential miRNA candidates belonging to miR168, miR2911, and miR156 families were identified from 23 406 ESTs in sweet potato. A total of 42 target genes were predicted and their probable functions were illustrated. Most of the newly identified miRNAs target transcription factors as well as genes involved in plant growth and development, signal transduction, metabolism, defense, and stress response. The identification of miRNAs and their targets is expected to accelerate the pace of miRNA discovery, leading to an improved understanding of the role of miRNA in development and physiology of sweet potato, as well as stress response.
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Budheswar
B
Dehury
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Debashis
D
Panda
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Jagajjit
J
Sahu
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Mousumi
M
Sahu
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Kishore
K
Sarma
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Madhumita
M
Barooah
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Priyabrata
P
Sen
Department of Agricultural Biotechnology; Assam Agricultural University; Assam, India.
Mahendra
M
Modi
D001483:Base Sequence; D003198:Computer Simulation; D017124:Conserved Sequence / Q000235:genetics*; D057225:Data Mining; D020224:Expressed Sequence Tags / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D027723:Ipomoea batatas / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D010802:Phylogeny
D035683:MicroRNAs
Expressed sequence tag; cleavage; miRNA; post-transcriptional gene silencing; sweet potato; transcription factors