02469nas a2200253   4500008004100000022001400041245011400055210006900169260007400238300001200312490000700324520154700331653000901878653002901887653003101916653000801947100002101955700002501976700002402001700002602025700002102051700002102072856012202093       2012                        eng d  a1380-374300aDevelopment of genomic simple sequence repeat markers for linseed using next-generation sequencing technology0 aDevelopment of genomic simple sequence repeat markers for linsee  aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcJUN  a597-6060 v303 a<p>Linseed (Linum usitatissimum L.) is regarded as a cash crop of tomorrow because of the presence of nutraceutically important alpha-linolenic acid (ALA) and lignan. However, only limited breeding progress has been made in this crop, mainly due to the lack of sufficient genetic and genomic resources. Among these, simple sequence repeats (SSR) are useful DNA markers for diversity analysis, genetic mapping and tagging traits because of their co-dominant and highly polymorphic nature. In order to develop SSR markers for linseed, we used three microsatellite isolation methods, viz., PCR Isolation of Microsatellite Arrays (PIMA), 5'-anchored PCR method, and Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO). The amplified products from these methods were pooled and sequenced using the 454 GS-FLX platform. A total of 36,332 reads were obtained, which assembled into 2,183 contigs and 2,509 singlets. The contigs and the singlets contained 1,842 microsatellite motifs, with dinucleotide motifs as the most abundant repeat type (54%) followed by trinucleotide motifs (44%). Based on this, 290 SSR markers were designed, 52 of which were evaluated using a panel of 27 diverse linseed genotypes. Among the three enrichment methods, the 5'-anchored PCR method was most efficient for isolation of microsatellites, while FIASCO was most efficient for developing SSR markers. We show the utility of next-generation sequencing technology for efficiently discovering a large number of microsatellite markers in non-model plants.</p>10aFlax10aMicrosatellite isolation10aNext-generation sequencing10aSSR1 aKale, Sandip, M.1 aPardeshi, Varsha, C.1 aKadoo, Narendra, Y.1 aGhorpade, Prakash, B.1 aJana, Murari, M.1 aGupta, Vidya, S.  uhttps://library.ncl.res.in/content/development-genomic-simple-sequence-repeat-markers-linseed-using-next-generation-003222nas a2200193   4500008004100000022001400041245014400055210006900199260008100268300000800349490000700357520242200364100002502786700002502811700002102836700002402857700002102881856012602902       2012                        eng d  a1471-216400aPhylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns0 aPhylogenomic analysis of UDP glycosyltransferase 1 multigene fam  a236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLANDbBIOMED CENTRAL LTDcMAY  a1750 v133 a<p>Background: The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. Results: Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged. Conclusions: Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.</p>1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S.  uhttps://library.ncl.res.in/content/phylogenomic-analysis-udp-glycosyltransferase-1-multigene-family-linum-usitatissimum-002528nas a2200277   4500008004100000022001400041245014300055210006900198260007100267300001400338490000700352520148300359653002501842653001601867653003201883653002601915653000801941653003701949100002501986700002502011700002102036700002402057700002002081700002102101856012802122       2012                        eng d  a1535-389300aProteome profiling of flax (linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development0 aProteome profiling of flax linum usitatissimum seed characteriza  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcDEC  a6264-62760 v113 a<p>Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of ID-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.</p>10aalpha-linolenic acid10acarbon flux10aDigital expression analysis10aflax seed development10aMSE10asecoisolariciresinol diglucoside1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aKadoo, Narendra, Y.1 aGiri, Ashok, P.1 aGupta, Vidya, S.  uhttps://library.ncl.res.in/content/proteome-profiling-flax-linum-usitatissimum-seed-characterization-functional-metabolic-002427nas 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-0