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De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts. PLoS One. 2014; 9: e102155. doi: 10
- 1371/journal.pone.0102155 PMID: 25025767
"... The floral transcriptome of Orchis italica, a wild orchid species, was obtained using Illumina RNA-seq technology and specific de novo assembly and analysis tools. More than 100 million raw reads were processed resulting in 132,565 assembled transcripts and 86,079 unigenes with an average length of ..."
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The floral transcriptome of Orchis italica, a wild orchid species, was obtained using Illumina RNA-seq technology and specific de novo assembly and analysis tools. More than 100 million raw reads were processed resulting in 132,565 assembled transcripts and 86,079 unigenes with an average length of 606 bp and N50 of 956 bp. Functional annotation assigned 38,984 of the unigenes to records present in the NCBI non-redundant protein database, 32,161 of them to Gene Ontology terms, 15,775 of them to Eukaryotic Orthologous Groups (KOG) and 7,143 of them to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The in silico expression analysis based on the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was confirmed by real-time RT-PCR experiments on 10 selected unigenes, which showed high and statistically significant positive correlation with the RNA-seq based expression data. The prediction of putative long non-coding RNAs was assessed using two different software packages, CPC and Portrait, resulting in 7,779 unannotated unigenes that matched the threshold values for both of the analyses. Among the predicted long non-coding RNAs, one is the homologue of TAS3, a long non-coding RNA precursor of trans-acting small interfering RNAs (ta-siRNAs). The differential expression pattern observed for the selected putative long non-coding RNAs suggests their possible functional role in different floral tissues.
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"... Knockdown of a JmjC domain-containing gene JMJ524 confers altered gibberellin responses by transcriptional regulation of GRAS protein lacking the DELLA domain genes in tomato ..."
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Knockdown of a JmjC domain-containing gene JMJ524 confers altered gibberellin responses by transcriptional regulation of GRAS protein lacking the DELLA domain genes in tomato
Knockdown of a JmjC domain-containing gene JMJ524
"... confers altered gibberellin responses by transcriptional regulation of GRAS protein lacking the DELLA domain genes in tomato ..."
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confers altered gibberellin responses by transcriptional regulation of GRAS protein lacking the DELLA domain genes in tomato
Article Development and Characterization of Transcription Factor Gene-Derived Microsatellite (TFGM) Markers in Medicago truncatula and Their Transferability in Leguminous and Non-Leguminous Species
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Functional Analysis of a Pomegranate (Punica granatum L.) MYB Transcription Factor Involved in the Regulation of Anthocyanin
, 2015
"... Land plants possess successful mechanisms for responding to environmental challenges. In these elab-orate systems, transcriptional regulation plays critical roles due to their broad adaptation and coordinately modulates of hundreds of different genes within regu-latory networks. Transcription factor ..."
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Land plants possess successful mechanisms for responding to environmental challenges. In these elab-orate systems, transcriptional regulation plays critical roles due to their broad adaptation and coordinately modulates of hundreds of different genes within regu-latory networks. Transcription factors are powerful means for regulation of gene expression and consist of at least four distinct domains, DNA binding domain, nuclear localization signal (NLS), transcription activa-tion domain, and oligomerization site, which operate together to control many physiological processes (1). Based on the specific conserved DNA-binding domains, the transcription factor genes can be classi-fied into different families or super-families (2). The MYB transcription factor superfamily is a group of
ARTICLE
"... Cotton fibres are unusually long, single-celled epidermal seed trichomes and a model for plant cell growth, but little is known about the regulation of fibre cell elongation. Here we report that a homeodomain-leucine zipper (HD-ZIP) transcription factor, GhHOX3, controls cotton fibre elongation. GhH ..."
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Cotton fibres are unusually long, single-celled epidermal seed trichomes and a model for plant cell growth, but little is known about the regulation of fibre cell elongation. Here we report that a homeodomain-leucine zipper (HD-ZIP) transcription factor, GhHOX3, controls cotton fibre elongation. GhHOX3 genes are localized to the 12th homoeologous chromosome set of allotetraploid cotton cultivars, associated with quantitative trait loci (QTLs) for fibre length. Silencing of GhHOX3 greatly reduces (480%) fibre length, whereas its over-expression leads to longer fibre. Combined transcriptomic and biochemical analyses identify target genes of GhHOX3 that also contain the L1-box cis-element, including two cell wall loosening protein genes GhRDL1 and GhEXPA1. GhHOX3 interacts with GhHD1, another homeodomain protein, resulting in enhanced transcriptional activity, and with cotton DELLA, GhSLR1, repressor of the growth hormone gibberellin (GA). GhSLR1 interferes with the GhHOX3–GhHD1 interaction and represses target gene transcription. Our results uncover a novel mechanism whereby a homeodomain protein transduces GA signal to promote fibre
Article In Silico Analysis of the Genes Encoding Proteins that Are Involved in the Biosynthesis of the RMS/MAX/D Pathway Revealed New Roles of Strigolactones in Plants
"... Abstract: Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. ..."
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Abstract: Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates
Original article GraP: platform for functional genomics analysis
"... Cotton (Gossypium spp.) is one of the most important natural fiber and oil crops world-wide. Improvement of fiber yield and quality under changing environments attract much attention from cotton researchers; however, a functional analysis platform integrating omics data is still missing. The success ..."
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Cotton (Gossypium spp.) is one of the most important natural fiber and oil crops world-wide. Improvement of fiber yield and quality under changing environments attract much attention from cotton researchers; however, a functional analysis platform integrating omics data is still missing. The success of cotton genome sequencing and large amount of available transcriptome data allows the opportunity to establish a comprehensive analysis platform for integrating these data and related information. A comprehensive database, Platform of Functional Genomics Analysis in Gossypium raimondii (GraP), was constructed to provide multi-dimensional analysis, integration and visualization tools. GraP includes updated functional annotation, gene family classifications, protein–protein interaction networks, co-expression networks and microRNA–target pairs. Moreover, gene set enrichment analysis and cis-element significance analysis tools are also pro-vided for gene batch analysis of high-throughput data sets. Based on these effective services, GraP may offer further information for subsequent studies of functional genes and in-depth analysis of high-throughput data. GraP is publically accessible at
