title: A genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L.
abstract: Micro RNAs (miRNAs) are involved in diverse biological processes including adaptive response towards abiotic stresses. To unravel small RNAs and more specifically miRNAs that can potentially regulate determinants of abiotic stress tolerance, next generation sequencing of B. juncea seedlings subjected to high temperature, high salt and drought conditions was carried out. With the help of UEA sRNA workbench software package, 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Ankur R
authors.initials: AR
authors.lastname: Bhardwaj
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Gopal
authors.initials: G
authors.lastname: Joshi
authors.affiliation: Department of Plant Molecular Biology, University of Delhi, South Campus, Delhi, India.
authors.forename: Ritu
authors.initials: R
authors.lastname: Pandey
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Bharti
authors.initials: B
authors.lastname: Kukreja
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Shailendra
authors.initials: S
authors.lastname: Goel
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Arun
authors.initials: A
authors.lastname: Jagannath
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Amar
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Plant Molecular Biology, University of Delhi, South Campus, Delhi, India.
authors.forename: Surekha
authors.initials: S
authors.lastname: Katiyar-Agarwal
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Manu
authors.initials: M
authors.lastname: Agarwal
mesh_terms: D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D017124:Conserved Sequence; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D018749:RNA, Plant / Q000235:genetics; D015203:Reproducibility of Results; D054712:Salinity; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant