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      Phylogeny and Density Dynamics of Wolbachia Infection of the Health Pest Paederus fuscipes Curtis (Coleoptera: Staphylinidae)

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          Abstract

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          Wolbachia pipientis is a maternally inherited endosymbiont of arthropods and filarial nematodes, and was reported to occur in Paederus fuscipes, a beetle that causes dermatitis linearis and conjunctivitis in humans when they come in contact with skin. In this study, we report the phylogenetic position and density dynamics of Wolbachia in P. fuscipes. The phylogeny of Wolbachia, based on an analysis of MLST genotyping, showed that Wolbachia from P. fuscipes belongs to supergroup B. Quantitative PCR indicated that the infection density in adults was higher than in any other life stage (egg, larva or pupa), and that reproductive tissue in adults had the highest infection densities, with similar densities in the sexes. These findings provide a starting point for understanding Wolbachia infection dynamics in P. fuscipes, and interactions with other components of the microbiota.

          Abstract

          The maternally inherited obligate intracellular bacteria Wolbachia infects the reproductive tissues of a wide range of arthropods and affects host reproduction. Wolbachia is a credible biocontrol agent for reducing the impact of diseases associated with arthropod vectors. Paederus fuscipes is a small staphylinid beetle that causes dermatitis linearis and conjunctivitis in humans when they come into contact with skin. Wolbachia occur in this beetle, but their relatedness to other Wolbachia, their infection dynamics, and their potential host effects remain unknown. In this study, we report the phylogenetic position and density dynamics of Wolbachia in P. fuscipes. The phylogeny of Wolbachia based on an analysis of MLST genotyping showed that the bacteria from P. fuscipes belong to supergroup B. Quantitative PCR indicated that the infection density in adults was higher than in any other life stage (egg, larva or pupa), and that reproductive tissue in adults had the highest infection densities, with similar densities in the sexes. These findings provide a starting point for understanding the Wolbachia infection dynamics in P. fuscipes, and interactions with other components of the microbiota.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              UFBoot2: Improving the Ultrafast Bootstrap Approximation

              Abstract The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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                Author and article information

                Journal
                Insects
                Insects
                insects
                Insects
                MDPI
                2075-4450
                11 September 2020
                September 2020
                : 11
                : 9
                : 625
                Affiliations
                [1 ]Laboratory of Environmental Entomology, College of Life Sciences, Shanghai Normal University, Xuhui, Shanghai 200234, China; gretchen9505@ 123456163.com (C.G.); hujiayao@ 123456shnu.edu.cn (J.H.); zhaozimiao818926@ 123456163.com (Z.Z.); mashuojia@ 123456126.com (S.M.); shenlismile@ 123456163.com (L.S.); fangjie2019@ 123456163.com (J.F.); ywd@ 123456shnu.edu.cn (W.Y.)
                [2 ]School of BioSciences, The University of Melbourne, Bio21 Institute, Parkville, VIC 3052, Australia; Ary@ 123456unimelb.edu.au
                [3 ]Shanghai Zoological Park, Changning, Shanghai 200335, China; zzzjjq@ 123456gmail.com
                Author notes
                [* ]Correspondence: jiangwb@ 123456shnu.edu.cn
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0001-9497-7645
                https://orcid.org/0000-0002-5548-7253
                Article
                insects-11-00625
                10.3390/insects11090625
                7564247
                32932887
                9bfd1886-3668-4eae-b0e4-783d030b879b
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 30 July 2020
                : 08 September 2020
                Categories
                Article

                paederus fuscipes,wolbachia infection,phylogeny,density dynamics

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