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      The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation.

            Beetles represent almost one-fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre-Cretaceous origin of more than 100 present-day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.
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              Ethylene-induced stomatal closure in Arabidopsis occurs via AtrbohF-mediated hydrogen peroxide synthesis.

              Ethylene is a plant hormone that regulates many aspects of growth and development. Despite the well-known association between ethylene and stress signalling, its effects on stomatal movements are largely unexplored. Here, genetic and physiological data are provided that position ethylene into the Arabidopsis guard cell signalling network, and demonstrate a functional link between ethylene and hydrogen peroxide (H(2)O(2)). In wild-type leaves, ethylene induces stomatal closure that is dependent on H(2)O(2) production in guard cells, generated by the nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) oxidase AtrbohF. Ethylene-induced closure is inhibited by the ethylene antagonists 1-MCP and silver. The ethylene receptor mutants etr1-1 and etr1-3 are insensitive to ethylene in terms of stomatal closure and H(2)O(2) production. Stomata of the ethylene signalling ein2-1 and arr2 mutants do not close in response to either ethylene or H(2)O(2) but do generate H(2)O(2) following ethylene challenge. Thus, the data indicate that ethylene and H(2)O(2) signalling in guard cells are mediated by ETR1 via EIN2 and ARR2-dependent pathway(s), and identify AtrbohF as a key mediator of stomatal responses to ethylene.

                Author and article information

                Systematic Entomology
                Syst Entomol
                June 27 2019
                January 2020
                September 02 2019
                January 2020
                : 45
                : 1
                : 188-204
                [1 ]Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of Sciences Beijing China
                [2 ]Department of Life SciencesNatural History Museum London U.K.
                [3 ]Grupo de Ecología y Evolución en IslasInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain
                [4 ]Departamento de Zoología, Facultad de BiologíaUniversidad de Santiago de Compostela Santiago de Compostela Spain
                [5 ]Department of EntomologyChina Agricultural University Beijing China
                [6 ]Beijing Advanced Innovation Centre for Food Nutrition and Human HealthChina Agricultural University Beijing China
                [7 ]BGI‐Shenzhen Shenzhen China
                [8 ]China National GeneBank, BGI‐Shenzhen Shenzhen China
                [9 ]State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect PestsZhejiang University Hangzhou China
                [10 ]Department of Life SciencesImperial College London Ascot U.K.
                © 2020





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