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      Natural resistance-associated macrophage proteins (NRAMPs) are involved in cadmium enrichment in peanut (Arachis hypogaea L.) under cadmium stress

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          Abstract

          Cadmium (Cd) is a hazardous heavy metal, and Cd pollution has become a serious problem worldwide. Peanut ( Arachis hypogaea L.) is an important oil crop in the world and has a strong capacity to accumulate Cd in soil. The natural resistant-associated macrophage protein (NRAMP) plays an important part in the absorption and transportation of Cd in plants. To date, the NRAMP family in peanut is ill-informed. In the present study, 29 AhNRAMPs were identified and were classified into three groups and fourteen proteins in group 1 (G1), ten proteins in group 2 (G2) and five proteins in group 3 (G3). There are 71-1347 amino acids in AhNRAMPs. Most of the AhNRAMPs exhibited tissue-specific expression patterns. For instance, AhNRAMP10 and AhNRAMP26 from G1 were highly expressed in roots, G2 genes in shoots and leaves and G3 genes in shoots. The transcriptional levels of AhNRAMPs in roots can be regulated by Cd. Notably, 55% of (16) AhNRAMPs genes were upregulated in peanut roots and positively responded to Cd stress. It’s worth noting that the relative expressions of AhNRAMP2 and AhNRAMP11, which were increased by 6.9-fold and 14.1-fold at 3 h in roots of Cd-enriched variety under Cd stress while decreasing by 44% and 25% at the same time in Cd sensitive variety. In a word, the comprehensive research of the AhNRAMP family provides insights into the capacity of Cd enrichment in peanut.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            TBtools - an integrative toolkit developed for interactive analyses of big biological data

            The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
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              psRNATarget: a plant small RNA target analysis server (2017 release)

              Abstract Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility. This update enhances its analytical performance by developing a new scoring schema that is capable of discovering miRNA–mRNA interactions at higher ‘recall rates’ without significantly increasing total prediction output. The scoring procedure is customizable for the users to search both canonical and non-canonical targets. This update also enables transmitting and analyzing ‘big’ data empowered by (a) the implementation of multi-threading chunked file uploading, which can be paused and resumed, using HTML5 APIs and (b) the allocation of significantly more computing nodes to its back-end Linux cluster. The updated psRNATarget server has clear, compelling and user-friendly interfaces that enhance user experiences and present data clearly and concisely. The psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/.
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                Author and article information

                Journal
                Plant Growth Regulation
                Plant Growth Regul
                Springer Science and Business Media LLC
                0167-6903
                1573-5087
                April 2024
                October 20 2023
                April 2024
                : 102
                : 3
                : 619-632
                Article
                10.1007/s10725-023-01091-0
                d4688258-d98e-480b-b8f9-cdba0efa778f
                © 2024

                https://creativecommons.org/licenses/by/4.0

                https://creativecommons.org/licenses/by/4.0

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