Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness

Gasdermin D (GSDMD) is a newly discovered pyroptosis executive protein, which can be cleaved by inflammatory caspases and is essential for secretion of IL-1β, making it a critical mediator of inflammation. However, the precise role of GSDMD in carcinogenesis remains nearly unknown. Considering the vital role of inflammation in tumorigenesis, we investigated the biological function of GSDMD in non-small cell lung cancer (NSCLC). Our study demonstrated that the GSDMD protein levels were significantly upregulated in NSCLC compared to these levels in matched adjacent tumor specimens. Higher GSDMD expression was associated with aggressive traits including larger tumor size and more advanced tumor-node-metastasis (TNM) stages. In addition, high GSDMD expression indicated a poor prognosis in lung adenocarcinoma (LUAD), but not in squamous cell carcinoma (LUSC). Knockdown of GSDMD restricted tumor growth in vitro and in vivo. Notably, intrinsic and extrinsic activation of pyroptotic (NLRP3/caspase-1) signaling in GSDMD-deficient tumor cells induced another type of programmed cell death (apoptosis), instead of pyroptosis. GSDMD depletion activated the cleavage of caspase-3 and PARP, and promoted cancer cell death via intrinsic mitochondrial apoptotic pathways. In addition, co-expression analyses indicated a correlation between GSDMD and EGFR/Akt signaling. Collectively, our results revealed a crosstalk between pyroptotic signaling and apoptosis in tumor cells. Knockdown of GSDMD attenuated tumor proliferation by promoting apoptosis and inhibiting EGFR/Akt signaling in NSCLC. In conclution, GSDMD is an independent prognostic biomarker for LUAD.

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De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.

BackgroundGrowth regulating factors (GRFs) have been shown to play important roles in plant growth and development. GRF genes represent a large multigene family in plants. Recently, genome-wide structural and evolutionary analyses of the GRF gene families in Arabidopsis, rice, and maize have been reported. Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables for agricultural production, and a full genome assembly for this plant has recently been released. However, to our knowledge, the GRF gene family from Chinese cabbage has not been characterized in detail.ResultsIn this study, genome-wide analysis was carried out to identify all the GRF genes in Chinese cabbage. Based on the complete Chinese cabbage genome sequence, 17 nonredundant GRF genes, named BrGRFs, were identified and classified into six groups. Phylogenetic analysis of the translated GRF protein sequences from Chinese cabbage, Arabidopsis, and rice indicated that the Chinese cabbage GRF proteins were more closely related to the GRF proteins of Arabidopsis than to those of rice. Expression profile analysis showed that the BrGRF genes had uneven transcript levels in different organs or tissues, and the transcription of most BrGRF genes was induced by gibberellic acid (GA3) treatment. Additionally, over-expression of BrGRF8 in transgenic Arabidopsis plants increased the sizes of the leaves and other organs by regulation of cell proliferation.ConclusionsThe data obtained from this investigation will contribute to a better understanding of the characteristics of the GRF gene family in Chinese cabbage, and provide a basis for further studies to investigate GRF protein function during development as well as for Chinese cabbage-breeding programs to improve yield and/or head size.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-807) contains supplementary material, which is available to authorized users.

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Previous studies have showed that the VQ motif–containing proteins in Arabidopsis thaliana and Oryza sativa play an important role in plant growth, development, and stress responses. However, little is known about the functions of the VQ genes in Brassica rapa (Chinese cabbage). In this study, we performed genome-wide identification, characterization, and expression analysis of the VQ genes in Chinese cabbage, especially under adverse environment. We identified 57 VQ genes and classified them into seven subgroups (I–VII), which were dispersedly distributed on chromosomes 1 to 10. The expansion of these genes mainly contributed to segmental and tandem duplication. Fifty-four VQ genes contained no introns and 50 VQ proteins were less than 300 amino acids in length. Quantitative real-time PCR showed that the VQ genes were differentially expressed in various tissues and during different abiotic stresses and plant hormone treatments. This study provides a comprehensive overview of Chinese cabbage VQ genes and will benefit the molecular breeding for resistance to stresses and disease, as well as further studies on the biological functions of the VQ proteins.