02427nas a2200301   4500008004100000022001400041245011800055210006900173260005700242300001400299490000800313520138600321653003201707653001701739653001201756653001001768653002801778653002201806100002501828700002501853700002101878700001701899700002101916700001601937700002101953700002401974856012701998       2013                        eng d  a0032-093500aGenome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)0 aGenomewide identification and characterization of microRNA genes  a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcAPR  a1149-11610 v2373 a<p>MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.</p>10aDigital expression analysis10aGene cluster10aLinseed10amiRNA10aMiRNA target transcript10aPromoter analysis1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aQiu, Shuqing1 aRollins, Meaghen1 aDatla, Raju1 aGupta, Vidya, S.1 aKadoo, Narendra, Y.  uhttps://library.ncl.res.in/content/genome-wide-identification-and-characterization-microrna-genes-and-their-targets-flax-002468nas a2200265   4500008004100000022001400041245015900055210006900214260012000283300001000403490000700413520142200420653000901842653003001851653001901881653001201900653002601912653002201938100002101960700002501981700002502006700002102031700002402052856012602076       2013                        eng d  a0831-279600aGenome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure0 aGenomewide identification and characterization of nucleotide bin  a1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADAbCANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESScFEB  a91-990 v563 a<p>Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.</p>10aFlax10ain silico gene expression10amotif analysis10aNBS-LRR10aPhylogenetic analysis10aPromoter analysis1 aKale, Sandip, M.1 aPardeshi, Varsha, C.1 aBarvkar, Vitthal, T.1 aGupta, Vidya, S.1 aKadoo, Narendra, Y.  uhttps://library.ncl.res.in/content/genome-wide-identification-and-characterization-nucleotide-binding-site-leucine-rich-002571nas a2200241   4500008004100000022001400041245009300055210006900148260000800217300000700225490000700232520178400239653001902023653001802042653001602060653001702076653002102093100002102114700002202135700002502157700002202182856012502204       2021                        eng d  a2190-572X00aGlucosinolate induces transcriptomic and metabolic reprogramming in Helicoverpa armigera0 aGlucosinolate induces transcriptomic and metabolic reprogramming  cJAN  a260 v113 a<p>Glucosinolates protect plants from herbivory. Lepidopteran insects have developed resistance to glucosinolates which is well studied. However, the molecular effects of glucosinolate intake on insects are unexplored. To elucidate this, we performed transcriptomics and metabolomics of sinigrin-fed Helicoverpa armigera. Transcriptomics exhibits significant dysregulation of 2375 transcripts, of which 1575 are upregulated and 800 downregulated. Gene Ontology analysis of differentially expressed genes reveals that key hydrolases, oxidoreductases, and transferases are majorly affected. The negative impact of sinigrin is significant and localized in the endomembrane system and mitochondria. It also disturbs various biological processes such as regulation of protein metabolism and cytoskeletal organization. Furthermore, H. armigera putative myrosinase-like enzymes may catalyze the breakdown of sinigrin to allyl isothiocyanate (AITC). AITC targets the electron transport chain causing oxidative stress. KEGG pathway enrichment shows significant upregulation of oxidative phosphorylation, glutathione metabolism and amino acid metabolism. Activation of these pathways induces glutathione synthesis for sinigrin detoxification. Differential gene expression indicates upregulation of glutathione S-transferase and succinate dehydrogenase suggesting mitochondrial impact. Transcriptomics data correlated with metabolomics show changes in serine, methionine, ornithine, and other metabolite levels. It corroborates well with the transcript alterations supporting the increased glutathione production. Thus, our data suggest that sinigrin generates oxidative stress in H. armigera and insects alter their metabolic wiring to overcome sinigrin-mediated deleterious effects.</p>
10aDetoxification10aGlucosinolate10aGlutathione10amitochondria10aOxidative stress1 aJagdale, Shounak1 aTellis, Meenakshi1 aBarvkar, Vitthal, T.1 aJoshi, Rakesh, S.  uhttps://library.ncl.res.in/content/glucosinolate-induces-transcriptomic-and-metabolic-reprogramming-helicoverpa-armigera02902nas a2200301   4500008004100000022001400041245009800055210006900153260000900222300001100231490000800242520188100250653002502131653002402156653003702180653002702217653001802244653002602262100002502288700002502313700002302338700002302361700001802384700002302402700002202425700002702447856012602474       2024                        eng d  a0168-160500aGenome sequencing and protein modeling unraveled the 2AP biosynthesis in Bacillus cereus DB250 aGenome sequencing and protein modeling unraveled the 2AP biosynt  cMAR   a1106000 v4133 a<p>
	2-Acetyl-1-pyrroline (2AP) is an important and major flavor aroma compound responsible for the fragrance of basmati rice, cheese, wine, and several other food products. Biosynthesis of 2AP in aromatic rice and a few other plant species is associated with a recessive Betaine aldehyde dehydrogenase 2 (BADH2) gene. However, the literature is scant on the relationship between the functional BADH2 gene and 2AP biosynthesis in prokaryotic systems. Therefore, in the present study, we aimed to explore the functionality of the BADH2 gene for 2AP biosynthesis in 2AP synthesizing rice rhizobacterial isolate Bacillus cereus DB25 isolated from the rhizosphere of basmati rice (Oryza sativa L.). Full-length BcBADH2 sequence was obtained through whole genome sequencing (WGS) and further confirmed through traditional PCR and Sanger sequencing. Then the functionality of the BcBADH2 gene was evaluated in-silico through bioinformatics analysis and protein docking studies and further experimentally validated through enzyme assay. The sequencing and bioinformatics analysis results revealed a full-length 1485 bp BcBADH2 coding sequence without any deletion or premature stop codons. Full-length BcBADH2 was found to encode a fully functional protein of 54.08 kDa with pI of 5.22 and showed the presence of the conserved amino acids responsible for enzyme activity. The docking studies confirmed a good affinity between the protein and its substrate whereas the presence of BcBADH2 enzyme activity confirmed the functionality of BADH2 enzyme in B. cereus DB25. In conclusion, the findings of the present study suggest that B. cereus DB25 is able to synthesize 2AP despite a functional BADH2 gene and there may be a different molecular mechanism responsible for 2AP biosynthesis in bacterial systems, unlike that found in aromatic rice and other eukaryotic plant species.</p>
10a2-Acetyl-1-pyrroline10aBasmati rice flavor10aBetaine aldehyde dehydrogenase 210aProtein-ligand docking10aRhizobacteria10aWhole-genome sequence1 aDhondge, Harshal, V.1 aBarvkar, Vitthal, T.1 aDastager, Syed, G.1 aDharne, Mahesh, S.1 aRajput, Vinay1 aPable, Anupama, A.1 aHenry, Robert, J.1 aNadaf, Altafhusain, B.  uhttps://library.ncl.res.in/content/genome-sequencing-and-protein-modeling-unraveled-2ap-biosynthesis-bacillus-cereus-db25