Sisymbrium austriacum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA175834 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR576092_1.fastq.gz | Fastqsanger.gz | |||
| SRR576092_2.fastq.gz | Fastqsanger.gz |
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Project description:Sisymbrium irio Genome sequencing and assembly
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Project description:Resistance to the phenoxy synthetic auxin herbicide 2,4-D is conferred by a deletion mutation in the degron tail of IAA2. An RNA-Seq experiment was used to assemble a reference transcriptome for the weed species Sisymbrium orientale, to quantify gene expression, and to identify sequence variants in the alignments. A 27 bp deletion was identified in the IAA2 gene. Forward genetics supported the role of this deletion mutation in resistance. The IAA2 deletion allele was transformed into Arabidopsis thaliana to confirm that it conferred 2,4-D resistance.
2020-10-08 | GSE159202 | GEO
Project description:The complete chloroplast genome of Sisymbrium irio was determined. The length of the complete chloroplast genome is 154,001 bp. The whole chloroplast genome consists of 83,891 bp long single copy (LSC) and 17,630 bp small single copy (SSC) regions, separated by a pair of 26,240 bp inverted repeat (IR) regions. The S. irio chloroplast genome encodes 112 annotated known unique genes including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic position of S. irio is sister to Brassiceae and Thlaspideae.
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Project description:Sisymbrium altissimum (S. altissimum), belonging to the family Brassicaceae, can grow in soils of all textures, even sand. Here, we reported the complete chloroplast (cp) genome of S. altissimum using Illumina sequencing data. The cp genome exhibited a typical quadripartite cycle of 154,042 bp, composing of a pair of inverted repeats (IRs, 26,260 bp) separated by a large single-copy (LSC, 83,912 bp) region and a small single copy (SSC, 17,610 bp) region. A total of 132 genes (87 protein-coding genes, 37 tRNAs, and eight rRNAs) were annotated in this cp genome. Phylogenetic analysis revealed that S. altissimum was closely related to Sisymbrium irio.
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Project description:Resistance to the herbicide 2,4-D in Sisymbrium orientale conferred by a deletion mutation in the degron tail of IAA2
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Project description:Petal is not only the target of selection by horticulturalists to enhance the ornamental value of plants but also emerged as a unique model system for plant organogenesis studies. It is known that three major groups of pigments, betalains, carotenoids and anthocyanins, are responsible for the attractive natural display of flower colors. While carotenoids and betalains generally yield yellow or red colors, anthocyanins confer a diverse range of color from orange to red to violet and blue. In this study, we collected 11 species (Erysimum cheiri, Malcolmia maritime, Brassica oleracea, Raphanus sativus, Orychophragmus violaceus, Eruca sativa, Orychophragmus violaceus, Iberis amara, Aubrieta x cultorum, Lobularia maritime, Matthiola incana) belong to different tribe in Brassicaceae family with varied flower color and performed petal transcriptome analysis. de novo transcriptome assembly showed that average length of the contigs varied from 631bp in O. violaceus to 1212bp in Matthiola incana which indicated that the complexity of the genomes are different much. Protein homology between these species and those sequenced species in Brassicaceae family are consistent with the known phylogenetic relationships. However, O. violaceus has closer relationships with Sisymbrium irio than expected Brassica species. Clustering analysis of genes in anthocyanin and carotenoids synthesis pathway indicated that while silence or low expression of CCD4 (Carotenoid Cleavage Dioxygenase 4) leading to the yellow color formation in different species, purple or red color variation might result from different genes expression variation. These results not only provide transcriptome data for petal development study but also provide useful information for Brassica flower improvement for ornamental purpose.
2017-01-24 | GSE93879 | GEO
Project description:Sisymbrium officinale (L.) Scop. (hedge mustard) is a wild common plant of the Brassicaceae family. It is known as "the singers' plant" for its traditional use in treating aphonia and vocal disability. The plant is rich in glucosinolates and isothiocyanates; the latter has been demonstrated to be a strong agonist in vitro of the Transient Receptor Potential Ankirine 1 (TRPA1) channel, which is involved in the somatosensory perception of pungency as well as in the nociception pathway of inflammatory pain. Volatile ITCs are released by the enzymatic or chemical hydrolysis of GLSs (glucosinolates) during sample crushing and/or by the mastication of fresh plant tissues when the plant is used as an ingredient. Some functional food and drink model preparations have been realised: honey enriched with seeds and flowers, infusions, cold drink (voice drink), artisanal beer, and a fermented tea (kombucha). Using SPME-GCMS chromatography, we analysed samples of the plant and of the food preparations adopting conditions that simulate the release of isothiocyanates (ITCs) during oral assumption. Two active compounds, iso-propylisothiocyanate and 2-butylisothiocyanate, have been assayed. The concentration of ITCs varies according to temperature, pH, grinding conditions, and different plant organs used. Kombucha-type fermentation seems to eliminate the ITCs, whereas they are retained in beer. The ITCs' concentration is higher when entire seeds and flowers are used.
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Project description:Phytochemical investigation of the ethanolic extract of the aerial parts of Sisymbrium irio L. led to the isolation of four unsaturated fatty acids (1-4), including a new one (4), and four indole alkaloids (5-8). The structures of the isolated compounds were characterized with the help of spectroscopic techniques such as 1D, 2D NMR, and mass spectroscopy, and by correlation with the known compounds. In terms of their notable structural diversity, a molecular docking approach with the AutoDock 4.2 program was used to analyze the interactions of the identified fatty acids with PPAR-γ and the indole alkaloids with 5-HT1A and 5-HT2A, subtypes of serotonin receptors, respectively. Compared to the antidiabetic drug rivoglitazone, compound 3 acted as a potential PPAR-γ agonist with a binding energy of -7.4 kcal mol-1. Moreover, compound 8 displayed the strongest affinity, with binding energies of -6.9 kcal/mol to 5HT1A and -8.1 kcal/mol to 5HT2A, using serotonin and the antipsychotic drug risperidone as positive controls, respectively. The results of docked conformations represent an interesting target for developing novel antidiabetic and antipsychotic drugs and warrant further evaluation of these ligands in vitro and in vivo. On the other hand, an HPTLC method was developed to quantify α-linolenic acid in the hexane fraction of the ethanol extract of S. irio. The regression equation/correlation coefficient (r2) for linolenic acid was Y = 6.49X + 2310.8/0.9971 in the linearity range of 100-1200 ng/band. The content of α-linolenic acid in S. irio aerial parts was found to be 28.67 μg/mg of dried extract.
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Project description:After-ripening (AR) in Sisymbrium officinale seeds altered SoACS7, SoACO2, SoGA20ox2, SoGA3ox2, and SoGA2ox6 gene expression. Except for SoGA20ox2 expression, which sharply diminished, the expression of the other genes rose during development, particularly that of SoACS7. In contrast, only the SoACO2 and SoGA2ox6 transcripts increased with seed desiccation; the others decreased. AR increased the SoGA3ox2 transcript in dry seed, but dramatically decreased the SoACS7 transcript. At the onset of imbibition, AR inhibited SoACS7 and SoACO2 expression and stimulated that of SoGA20ox2, SoGA3ox2, and SoGA2ox6, demonstrating that the participation of ethylene (ET) and gibberellins (GAs) differs in after-ripened and non-after-ripened seeds. The inhibition of SoACO2 expression in the presence of GA(4+7), paclobutrazol (PB), inhibitors of ET synthesis and signalling (IESS), and notably ET+GA(4+7) indicated ET-GA cross-talk in non-after-ripened seeds. A positive effect of AR in reversing this inhibition was found. The idea of ET-GA cross-talk is also supported by the effect of ET on SoGA3ox2 expression, notably induced by the AR process. In contrast, SoGA20ox2 expression did not appear to be susceptible to AR. SoGA2ox6 expression, poorly known in seeds, suggests that AR prompted an up-regulation under all treatments studied, whereas in non-after-ripened seeds expression was down-regulated. On the other hand, the beta-mannanase (MAN) activity dramatically increased in dry after-ripened seed, being significantly boosted by ET. The absence of MAN inhibition by IESS suggests that although ET seems to be one of the factors controlling MAN, its presence did not appear to be essential. GA(4+7) only increased MAN in seeds which were after-ripened. Here, it is proposed that ET and GAs participate actively in establishing the AR process.
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